Best Payroll Software for Small Business.

Say hello to CheckMark Payroll, the most powerful and affordable payroll software for small business.

DIY desktop payroll software
Unlimited employees & unlimited payrolls
MICR check printing & ACH direct deposit Create ACH direct deposit files to submit to your bank or ACH provider for processing paychecks.
Print/E-file W2s and W3s
US-based payroll support

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Join 12000+ business owners

Trusted by more than 12000+ businesses

All your payroll tools and data — all under one roof.

The job is tough for business owners. Either you’re juggling various online payroll solutions, or you’re stuck with complex tools that are powerful but difficult to use. This means scattered payroll data, poor reporting, and too much time spent working around the software to try to make it “fit.” But it doesn’t have to be that way.

With Checkmark Payroll, all your payroll tools and data are stored and accessed from your desktop. You’ll save valuable time and get all the information you need to process payroll efficiently, increase employee morale, and avoid costly penalties.

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Run Payroll in 3 Easy Steps!

Enter Hours

Add or import payroll hours, select your pay period dates, and pay date.

Calculate Payroll

Review and calculate payroll for each employee individually or all at once.

Pay Employees

Print checks or pay employees online via ACH direct deposit.

Here's How CheckMark Payroll Can Benefit Your Business

Save Time

Automate payroll and concentrate on growing your business.

Save Money

Manage payroll yourself and save while doing it.
See Payroll Pricing

Happy Employees

Pay employees accurately and on time to increase their productivity.

100% Accuracy

Deliver error-free paychecks, W-2s, and payroll reports.

Simplified Compliance

Stay in compliance with IRS laws and reporting requirements.

Streamline Payroll

Improve the efficiency of your company and employees.

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Enterprise-Level Features for Small Businesses.

Process Unlimited Employees

Whether you have 2 employees or 2000, our program lets you enter unlimited employees and process unlimited payrolls.

Unlimited Payroll Processing

Whatever your pay cycle may be, our program allows you to complete as many payroll runs as you need.

Easy ACH Direct Deposit

Create ACH files and submit them to your bank or ACH provider to deposit paychecks directly into employees' accounts.

MICR Check Printing

Print MICR encoded checks on blank check stock and give more privacy and control to your employees.

Simplified W2 Reporting

Print or e-file W-2 and W-3 forms to the SSA and most states. You can also print 941, 940, 944, and 943 forms.

US-Based Payroll Support

Get help fast with our knowledgeable technical support team. Contact us by phone, email or live chat.

Who is CheckMark Payroll for?

We are a small business ourselves; we understand small business needs, and payroll processing is in our DNA.

CheckMark Payroll has the ability to serve almost any business segment. We have worked really hard to build the powerful payroll software that can handle anything from basic payroll to complex payroll requirements.

It does not matter what kind of business you have, CheckMark Payroll has all the features you would expect from a high-priced enterprise payroll system.

With 36+ years of experience in the payroll industry and one of the first companies to roll out payroll software in the ’80s, you can trust us to take care of your payroll and taxes.

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Employers

HR Managers

Accountants

Rated the best

Here Is What Our Customers Have to Say

Thoroughly pleased with your software and support...

I have been using CheckMark Payroll and 1099 Print for over ten years and am so thoroughly pleased with your products and service that I will continue to purchase them. You support the products excellently and I especially like that when there is an update, you release it release it immediately. Thank you for your efforts.

John, Maryland

Wonderful alternative to QuickBooks payroll...

I use Checkmark Payroll. Your software has been a wonderful alternative to Quickbooks payroll. It allows me to save my clients a lot of money and not only is it easy to use, but it allows for importing all the payroll data into Quickbooks. This is again saves time and money.

Julie, Illinois

Excellent

We are always pleased with the ease of use of the CheckMark platform. It is always nice knowing it automatically updates taxes for federal and state, and transferring to our accounting software is a breeze! We are happy with the product.

james, Colorado

Saved us time and money...

Prior to CheckMark our company was outsourcing our payroll, and now we don't have to do that anymore. CheckMark Payroll has saved us time and money by making it so easy for me to create and submit payroll all the while knowing I can trust the taxes withheld for my specific state! Also, the software makes it easy for me to create and submit my quarterly and annual reports.

Kristina, Minnesota

Thousands of Business Owners Trust CheckMark Payroll

For over 40 years, CheckMark has been committed to providing the most reliable, user-friendly and cost-effective business solutions to small and medium-sized businesses. CheckMark pioneered Payroll and accounting software for the Mac platform in the 80's. Since then, we have developed cross-platform programs for payroll, accounting, 1099 and 1095.

Recognizing the growing demand for online payroll and the changing landscape of business operations, CheckMark also launched a cloud payroll platform to provide businesses with greater flexibility, accessibility, and efficiency in managing their payroll processes.

Our top priority is to develop high quality business solutions that are simple to use and are priced with the small and medium sized business in mind. We are proud of our achievements and remain committed to providing the most trusted and reliable solutions to run your business.

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Designed and Developed by Payroll Experts

Our payroll experts have worked hard to build a robust and powerful payroll software that suits any size business. With 40 years of experience in the Payroll industry rest assured you are in safe hands.

Easy-To-Use & Intuitive Design

CheckMark payroll’s simple user interface allows users to process payrolls quickly and accurately. The program is packed with powerful Payroll resources so that you can be up and running in no time.

Fixed Pricing, No Surprises

CheckMark’s one-time low annual fee is all-inclusive. Our competitors charge additional fees for initial setup, tech support, additional employees, direct deposit, MICR encoded checks, printing or e-Filing W2s & W3s, etc.

IRS Compliant

It is difficult to keep up with constantly changing Payroll and tax regulations. Our dedicated staff of Payroll professionals ensures that you stay in compliance with tax laws, IRS regulations, and reporting requirements.

Award-Winning Software

CheckMark Payroll has been recognized as one of the Top 10 Payroll Solutions in USA for small and medium size businesses by HR Tech Outlook Magazine. CheckMark Payroll was chosen based on its comprehensive functionality, cost effectiveness, and scalability.

US-based Tech Support

CheckMark provides certified payroll support representatives, who know the program in and out, and can help you resolve your questions quickly. You may reach us by phone, email or fax.

Payroll Reporting Made Easy

Payroll taxes are an important part of your business. CheckMark Payroll takes the stress out of tax filing by providing a variety of detailed payroll reports for small business owners at no extra charge. You get access to 40-plus payroll reports that can be viewed on screen, printed, filed and saved as a text or .xls file.

Employee Information

Employee Information Reports provide all the critical information about employees' personal data, salary or hourly rates, tax setups, additional incomes, deductions, and much more.

The Personal Information report shows the employee personal data, including name, address, phone number, Social Security number, birth date, employee number, employment status, email address and default department.

The Wage Information report shows the employee’s salary or hourly rates, pay frequency, hire date, last raise date, termination date, accrued hours available, and department/job distribution percentages, and direct deposit if marked.

The Tax Information report shows the tax set up for the employee including, W-2 options, selected federal, state, SUTA state, local tables, and more.

The Income/Deduction Information report shows the Additional Information Income and Deduction categories and their associated definitions that have been set up for the selected employees.

Employee Earnings

Employee Earnings Reports provide the employer with all the employee data such as YTD income, net pay, accrued hours, vacation and sick pay, tax amounts, and much more.

For the range of check dates selected, the Earnings Register report shows the employee’s selected check period along with YTD income, deductions, taxes, and net pay, as well as any employer matching amounts. Totals for the company are listed at the end of the report. You can see this report arranged by department by selecting the By Department check box. You can also Sort Employees by their Last Name or Social Security #.

For the range of check dates selected, the Hours Register report shows the employee’s selected check period and year-to-date hours for hour categories as well as accrued hours available. You can also Sort Employees by their Last Name or Social Security #.

You can also get an Hours Register report that contains only Hours Worked. Simply check the Hours Worked Only box. This report is helpful in filling out worker’s compensation reports or SUTA reports in states where this information is required.

The Check Summary report shows an employee’s income, taxes, deductions, and net, vacation and sick pay for each check in the selected check dates. Totals for all categories are also shown by employee.

The Check Details report shows income, tax amounts, deductions, total tax amounts, total deductions, and net pay by check for each selected employee for the selected check dates. Totals for selected employees are listed at the end of the report.

Employee Paychecks

As the name suggests, Employee Paychecks Reports allow employers to track every detail related to their paychecks such as hourly rates, ACH Direct Deposit text files, Web Direct Deposit text files, ACH NPC Direct Deposit text files, and much more.

The Employee Check Register report shows check data for the selected check dates, including number of hours, hourly rates, income, deductions, net pay, and department/job distribution percentages and amounts. Company totals are shown at the bottom of the report, including 941 liability and the number of checks in the selected period.

The Posting Summary report shows check information in a summarized format and can be used to create manual journal entries in your accounting system. (You can also save the posting summary information as a text file that can be imported into an accounting program.) The net for each check is shown, along with totals for wages, income, taxes, and deductions.

Ledger accounts are also shown with their associated amounts. If you have ledger accounts set up for department or job wages and taxes, then the ledger accounts and amounts for each department or job are shown. The total debits and credits are shown on the last two lines.

CheckMark Payroll Software allows you to utilize direct deposit for your employees through your financial institution. Payroll creates an ACH file that you can submit directly to your bank. For more information on setting up CheckMark Payroll for Direct Deposit, see “ Using CheckMark Payroll for ACH Direct Deposit”. The ACH Direct Deposit text file contains only checks created for employees who are set up as Direct Deposit employees on the Personal tab of the Employees window.

You can export a file for use with National Payment Corporation’s Web Direct Deposit. For more information on Web Direct Deposit, see “ Using CheckMark Payroll for Web Direct Deposit”. the web direct deposit text file contains only checks for employees who are set up as direct deposit employees on the personal tab of the employees window.

You can export a file for use with National Payment Deposit Corporation’s Direct Deposit. For more information on ACH NPC Direct Deposit, see “ Using CheckMark Payroll for ACH NPC Direct Deposit ”. The ACH NPC Direct Deposit text file contains only checks for employees who are set up as Direct Deposit employees on the Personal tab of the Employees window.

Employer Payment

Employer Payments Reports allow you to view all the taxes withheld for Medicare and Social Security. View, print, or export journal entries to your favorite accounting programs such as CheckMark MultiLedger, QuickBooks, Quickens, Peachtree, MYOB, Connected, and much more.

The Check Register report shows check data for the selected month, including check number, check date, payee, payment description, and the check amount.

The Posting Summary report shows check information in a summarized format and can be used to create manual journal entries in your accounting system. (You can also save the posting summary information as a text file that can be imported into an accounting program.) Ledger accounts are shown with their associated amounts. The total debits and credits are shown on the last two lines.

Income and Deduction

The Income and Deduction Report is ideal for business owners who want to get an insight into how much they are spending for incomes and deductions for each or all employees.

The Deduction Detail reports shows the deduction name, employee SSN, employee name, employee deduction amount and employer match amount for individual checks, along with the total for each deduction. To view employee wages and employer wages in the same report, select the checkbox “Emp Wages & Empr Wages.”

The Income Detail report shows income name, employee social security number, employee name, check number, check date and total amount of income.

The Deduction Summary report shows the deduction name, employee SSN, employee name, deduction amount, match and total for the selected period. You can also sort the list by Last Name or Social Security #.

Department/Jobs

Monitoring employee and department performance is a fundamental task of any business owner. To assist in that process, our Department/Jobs Reports provide you with all data to empower you to make informed business decisions.

This report shows wages and number of hours for each department or job for each income category, including salary, all hour categories, and other income amounts. Totals for wages and hours for the selected report range appear after each department/job, and company totals appear at the end of the report.

This report shows detail for each department’s or job’s expense for wages and employer taxes (employer portions of Social Security, Medicare, FUTA, and SUTA). Details include employee name, check date, check number, hours, wages and employer taxes. Totals for wage expense and employer tax expense for the selected report range appear after each department/job, and company totals appear at the end of the report.

Federal Taxes

Federal Tax Reports are the most important tax filing reports for employers as it helps them to report the amount of income tax, Medicare, and Social Security taxes that are withheld from employees each year.

The Tax Summary report shows tax information, including employee names, total wages and tips, federal withholding, Advance EIC, Social Security wages, Social Security tips, and Medicare wages and tips for the selected quarter or current payroll year. You can use this tax data for filling out the Federal 941 form or use the annual report for filing form 943 or 944.

The Federal Taxes window prints the Form 941, Employer’s Quarterly Federal Tax Return form and gives you information that’s useful for filling out the form manually.

The Federal Taxes window prints the Form 943, Employer’s Annual Federal Tax Return for Agricultural Employees and gives you information that’s useful for filling out the form manually.

The Federal Taxes window prints the Form 944, Employer’s Annual Federal Tax Return and gives you information that’s useful for filling out the form manually.

940 FUTA Tax

CheckMark Payroll can produce form 940 as well as a wage summary and quarterly liability report. You can print completed Forms 940 on blank or pre-printed paper.

This report shows the total annual wages, wages exempt from FUTA, wages over the annual limit, and total taxable wages by employee.

This report shows total taxable wages per quarter by employee. In addition, this report shows total FUTA liability per quarter.

The 940 FUTA Taxes window prints the Form 940, Employers Annual Federal Unemployment (FUTA) Tax Return and gives you information that is useful for filling out the return manually.

State Taxes

The State Tax Reports allow you to view SUTA taxes to be paid for the 1st, 2nd, 3rd, and 4th quarters. For Californian employers, you can view and file the Quarterly Contribution Return and Report of Wages (DE 9) every quarter.

The SUTA report shows wages exempt from SUTA (state unemployment), wages subject to SUTA, wages in excess of the SUTA maximum, and SUTA taxable wages. It also shows your SUTA rate, SUTA tax amount, number of employees per month and number of employees in the pay period including the 12th of the month for each month of the quarter.

You can print a DE 9 form for filing with the EDD directly from CheckMark Payroll.

Employers who are set up with California’s EDD to file their Quarterly Wage and Withholding Reports electronically, can save a file from CheckMark Payroll to submit to the EDD in the DE-9 XML format. For more information on submitting the DE-9 XML information electronically, contact the EDD.

Employers who are set up with California’s EDD to file their Quarterly Wage and Withholding Reports electronically, can save a file from CheckMark Payroll to submit to the EDD in the DE-9C MMREF format. For more information on submitting the DE-9C MMREF information electronically, contact the EDD

CheckMark Payroll can create the New Work MMREF file. New York requires submission of the test file with notification that the test was certified and successfully processed. Contact the New York State Department of Tax and Finance for complete filing instruction. Additional information is included in NY Publication 911 available at https://www.tax.ny.gov/.

CheckMark Payroll can create the Mississippi ICESA file. Mississippi requires submission of the test file with notification that the test was certified and successfully processed.

W-2 and W-3 Statements

The W2 & W3 Statements Reports allow you to print W-2 and W-3 information on blank perforated sheets or pre-printed forms. You can also save your W-2/W-3 information in the EFW2 file format for electronic filing.

4-up Employee All Copies - This is for printing employee Copies B, C, and 2 on 4-up blank, perforated paper. 2-up Employer Copy A - This is for printing employer Copy A on plain paper (minimum 20 lb. weight). 2-up Employer Copy 1 - This is for printing employer Copy 1 on 2-up blank, perforated paper. 2-up Employer Copy D - This is for printing employer Copy D on 2-up blank, perforated paper.

2-up Employee Copy B - This is for printing employee Copy B on 2-up blank, perforated paper.2-up Employee Copy C - This is for printing employee Copy C on 2-up blank, perforated paper. 2-up Employee Copy 2 - This is for printing employee Copy 2 on 2-up blank, perforated paper.

This is for printing employee and employer W-2s on pre-printed W-2 forms.

Select this option for printing on a W-3 form on plain paper (minimum 20 lb. weight).

Select this option if you are printing on a pre-printed W-3form.

Select this option if you are required to file electronically with the Social Security Administration or your state.

Local Taxes

The Local Tax Report shows the employee's social security number, employee name, wages exempt from local taxes, total wages, wages subject to local tax, and amount of the local tax withheld. There are totals by local tax at the bottom of the report.

Experience CheckMark Payroll Software

An easy-to-use dashboard giving you quick access to setup, payroll processing, and reporting functions. A News Feed is constantly updated keeping you aware of important payroll changes. Other useful information is listed for quick reference including the number of active employees and where the data is being saved on your computer. Quick links in the upper right-hand corner provide simple, easy access to order paper products, contact support, browse the Knowledge Base, open the Payroll Manual, and much more!

Choose to use a Company or Trade Name to print on checks and reports. Also, an encrypted password keeps information away from prying eyes.

You can set up to 20 Additional Income categories for the company and assign up to 8 per employee. Choose from a list of pre-set categories to use or modify, or create your own.

You can set up to 30 Deduction categories for the company and assign up to 16 per employee. You can also set up an Employer Match for categories like a 401(k).

Sort employees by their last name, employee number, or department. Easily separate active or inactive employees, track accrued hours and assign specific Incomes and Deductions for each employee.

Input hours in an easy-to-follow, spreadsheet-type format or import them from your time and attendance system. Option to sort hourly employees first vs. those set up as salary for easier input.

This screen gives a breakdown of all hours, additional incomes, tax withholdings, and deductions for each employee regarding the specific paycheck for that designated pay period. Save the calculation for further review or you can create the check.

Print and format checks for all employees and check dates. You can also choose to email a stub if you do direct deposit. Print on pre-printed or blank check stock.

View earnings, hours, or check information for one employee, or all employees, or choose non-consecutive employees. You can also select one check date or choose a range. For example, select all check dates in Jan-Mar if you want a report that includes totals for 1st quarter.

View a check register or posting summary for one employee, or all employees, or choose non-consecutive employees. You can also select one check date or choose a range. For example, select all check dates in Jan-Mar if you want a report that includes totals for 1st quarter. This screen also allows you to export payroll data to other popular accounting programs such as QuickBooks and you can create an ACH file for handling Direct Deposit.

View a Tax Summary report or print out your quarterly 941, 943, or 944 reports.

Choose to print on blank or pre-printed W-2 forms. Print a W-3 or eFile the Federal EFW2 and most states.

Payroll Software FAQs

What is Payroll software?

Payroll software is a desktop or online payroll solution to manage, maintain and automate employee payments and tax compliance. You can use the software to enroll employees, withhold taxes and deductions, calculate wages, pay employees, file taxes, and maintain payroll records.

Payroll software is used by business owners, employers, HR managers, payroll professionals, and CPAs. No matter your company size, CheckMark Payroll is flexible enough to accommodate basic payroll to complex payroll requirements to streamline the entire life cycle of your payroll operations.

What are the benefits of payroll software?

Businesses use payroll software to automate their payroll processes. Some of the benefits of our employee payroll software include:

Decrease the chances of costly payroll errors.
Simplify tax filing processes.
Compliance with federal, state, and local laws.
Accurate payroll and wage calculations.
Huge time saver tool.
Reduced payroll costs.
Maintenance of payroll records.

Do I need payroll software for my small business?

Yes, we recommend small business owners buy payroll software for automating their payroll operations to save time and avoid costly errors. CheckMark Payroll is designed to make the payroll processes more simpler and accurate. From wage calculation to withholding taxes, our payroll system helps you pay employees accurately and stay compliant with the IRS.

Our software is 100% compliant with the most recent government mandates for the 2025 tax year. The 2025 version includes the latest IRS-approved tax forms, state and federal tax tables, as well as support and software patches released throughout the year, and much more.

Which payroll software is best for small businesses?

CheckMark Payroll of course! Our payroll program offers enterprise-level features to small businesses at a fraction of the cost. It includes high-end features like direct deposit and MICR encoding blank check stock printing. Calculate payroll, print payroll checks, and pay employer taxes in a few minutes. Satisfaction guaranteed!

You can process as many payrolls as you want for all your employees. As your business grows and you start hiring new employees, the payroll costs will always remain the same.

What type of businesses uses payroll software?

CheckMark Payroll Software is designed for small to medium size businesses — from accountants and financial firms to real estate companies, non-profits, hospitals, universities, and restaurants.

How to choose payroll software for your business?

When choosing payroll software for small business, you need to select software that suits your business requirements. Our business payroll software is a simple, flexible, and robust stand-alone payroll software that will grow as your business grows. It has all the features you would expect from a high-priced payroll system.

How much does payroll software cost?

The cost of payroll software depends on many factors such as employee size, software deployment, and the monthly/annual base fee of payroll vendors. CheckMark Payroll is an affordable in-house payroll system that allows unlimited employees and unlimited payrolls for one flat annual fee. CheckMark offers two payroll plans — CheckMark Payroll Pro and CheckMark Payroll Pro+. There are no extra costs or hidden fees. The base license for CheckMark Payroll software includes one company and one computer. To manage additional companies or install the software on more computers, you’ll need to purchase extra licenses: $50 per additional company and $99 per additional computer.

See Payroll Pricing

Can payroll software help reduce costs?

Yes, payroll software helps you save time and money by automating payroll tasks, paying employees on time, and filing taxes accurately. With CheckMark Payroll Software, you can save hundreds of dollars down the line. Whether you have 5 employees or 500 employees, the cost of our payroll system remains the same. Your employee and payroll records are safe and secure.

What size of businesses can use CheckMark Payroll?

Whether you are a startup or a growing business, our payroll system is robust enough to accommodate any number of employees, be it 2 or 2000, and the cost stays the same.

Is my payroll data secure?

CheckMark does not store or save your payroll data. Since CheckMark Payroll is on-premises payroll software, all your payroll data is encrypted and stored on your local computer. No other application or program can open the payroll files on your computer other than our payroll software. We recommend keeping our software, operating system, and anti-virus always up-to-date to avoid unauthorized access.

When can I start using payroll software?

You can start using our stand-alone payroll software at any time of the year. With CheckMark Payroll, just enter the YTD totals for your employees as of the last completed quarter, then enter after-the-fact checks for the current quarter, and you're all set! We offer payroll setup support to help you get up and running fast.