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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
  • Fast ACH direct deposit & MICR check printing
  • Print/E-file W2s and W3s
  • US-based payroll support
Try it Free for 60 Days
Join 12000+ business owners windowsmacOS
payroll software for small business

Desktop Version | Online Version

Trusted by more than 12000+ businesses

  • jw morton
  • cherokee and walker
  • martinez finance group
  • brien realty group
  • hatch furniture
  • pappas restaurant

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.

Try it Free for 60 Days

Run Payroll in 3 Easy Steps!

1 payroll hours

Enter Hours

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

Calculate Payroll

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

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.

Try it Free for 60 Days
desktop payroll software

Enterprise-Level Features for Small Businesses.

process unlimited employees

Process Unlimited Employees

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

Unlimited Payroll Processing

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

Easy ACH Direct Deposit

Delight your employees by depositing their paychecks securely right in their bank account with ACH direct deposit.
MICR check printing

MICR Check Printing

Print MICR encoded checks on blank check stock and give more privacy and control to your employees.
simplified W2 reporting

Simplified W2 Reporting

Print/E-File 941, 940, 944, 943, W-2, and W-3 formsto the SSA and most states without leaving the software.
US based payroll support

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.

Try it Free for 60 Days
payroll software for employers


HR managers

HR Managers

payroll software for accountants


Rated the best

  • G2
  • capterra
  • GetApp
  • top 10 payroll solution providers

Here Is What Our Customers Have to Say

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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

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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

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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

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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 39 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.

Try it Free for 60 Days
Our payroll experts have worked hard to build a robust and powerful payroll software that suits any size business. With 39 years of experience in the Payroll industry rest assured you are in safe hands.
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.
CheckMark’s one-time low annual fee is all-inclusive. Our competitors charge additional fees for initial setup, tech support, additional companies/stores, additional employees, direct deposit, MICR encoded checks, printing or e-Filing W2s & W3s, etc.
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.
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.
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.

Experience CheckMark Payroll Software

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!

company information Choose to use a Company or Trade Name to print on checks and reports. Also, an encrypted password keeps information away from prying eyes.
additional income 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.
deductions 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).
employees 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.
enter hours 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.

Payroll Software FAQs

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.

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.

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 2024 tax year. The 2024 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.

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 and companies. As your business grows and you start hiring new employees, the payroll costs will always remain the same.

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.

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.

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 companies, employees, and 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.

See Payroll Pricing

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.

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.

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.
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.
Yes, you can import payroll data from QuickBooks, Patriot Payroll, Gusto, Onpay, or any other payroll applications into CheckMark Payroll Software using a .txt or .csv file format.
There are no added costs. We include our entire payroll solution with your initial purchase. There are no hidden costs. You will get all the features and support for on flat annual fee.
As a CheckMark customer, you’ll have access to our knowledge base, payroll manual, and software support. You can request support using our live chat or email or by calling our support team at 970-225-0522.

No, our payroll program is available to companies operating and running their businesses in the USA. But you can use our Canadian payroll software to process payroll for Canadian employees.

SEE CheckMark Canada Desktop Payroll Software

No, there are no additional fees for e-filing W2s or 940 forms. All the features are included in one low annual cost.

Take Control of Your Payroll

Desktop payroll software designed and built for small businesses

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