Payroll and HR software that helps you focus on your cause

We know that your number one priority is working on your mission. That’s why OnPay gives nonprofits and charities extra time — and saves money — by paying employees, filing taxes, and helping out with HR. It’s just $40 + $6 per active employee, each month.


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  1. OnPay
  2. Payroll Software
  3. Industries
  4. Nonprofits and 501(c)(3)


Perfect for all nonprofits

Whether you’re a public charity, private foundation, or another form of nonprofit — we’ve got you covered. Our payroll and HR software makes it easy to pay W-2 employees, 1099 contractors, volunteers, and board members. And with 30+ years of experience, we get things right when it comes to tax withholdings, payments, and filing FUTA exemptions. Integrations with top accounting and time tracking software even help you keep the books (and back office) in order.

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Fast, purpose-driven payroll

  • Automated federal and state taxes ⁠— including handling of FUTA exemptions for 501(c)(3) organizations
  • Run payroll in a few clicks from any device
  • Handle multiple pay rates and overtime
  • Flexible permissions to delegate payroll tasks
  • Free account setup and support by payroll experts


HR tools to help nonprofits stay organized

Secure document storage

Keep your personnel files up to date ⁠— without any papercuts. Send HR documents to employees for e-signature, and keep it all stored in the cloud for easy access and record keeping.

Employee self-service

Speed up your hiring process with automated onboarding workflows. Employees can onboard themselves, view pay stubs, and update their personal details from their own employee account.

PTO management

Our built-in HR tools make it easy to track and manage PTO requests. Customize your accrual policies, Workers can submit time off requests for manager approval right from the app.

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Loved by nonprofits

“We love the ease and simplicity of OnPay. Especially as a nonprofit, so much of our time is focused on mission-related work that having a difficult payroll system won’t work. We switched over to OnPay and it was the best decision we could have made for our team!”


Estes Park Nonprofit Resource Center


$40 + $6 per employee each month

Fully transparent pricing, with no surprises or hidden fees.

  • Unlimited monthly pay runs in any state
  • Free migration of employee and prior wage data
  • One simple monthly fee for all your needs
  • No extra cost to integrate benefits and workers’ comp
  • Award-winning customer support via email, phone, and chat


Try the best payroll for nonprofit organizations

It’s easy to get started. Provide a little information about your organization and we’ll get you set up.

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Nonprofits and 501(c)(3) FAQs

  • How much does it cost for me to run payroll for my nonprofit organization?

    Our pricing is simple and competitive at a monthly fee of $40 + $6 per employee (or contractor), for just about everything OnPay does. Plus your first month is on us (that’s right your first month is free!)! Also, the low monthly rate includes our top-rated payroll and flexible HR tools.

  • How do you set up payroll for a non-profit organization?

    Generally, non-profit organizations must withhold federal income taxes from their employee’s wages and pay a matching amount. To calculate the amount to withhold from an employee’s paycheck, use their Form W-4, Employee’s Withholding Certificate, and reference IRS Publication 15 and Publication 15-A. For any specific questions on how to handle, you should catch up with your CPA or accounting department.

  • Do nonprofits have to pay payroll taxes?

    Yes, even with tax-exempt status, when nonprofits have employees they’re subject to the same payroll taxes as for-profit organizations. You must withhold federal income tax and FICA (Social Security and Medicare) taxes from employee paychecks as well as pay the employer portion of FICA taxes.

  • What is a 501(c)(3) and its purpose?

    According to the IRS, organizations described in section 501(c)(3) are commonly referred to as charitable organizations. To be tax-exempt under section 501(c)(3) of the Internal Revenue Code, an organization must be organized and operated exclusively for exempt purposes set forth in section 501(c)(3), and none of its earnings may inure to any private shareholder or individual.


    The organization must not be organized or operated for the benefit of private interests. If you are not sure if your organization falls under these designations, contact your CPA, bookkeeper or accounting personnel.

  • Can I pay myself if I run a nonprofit (and am I required to?)

    Yes, you are able to pay yourself. If you run a nonprofit, own an S-Corporation, a C-Corporation, or you’re an LLC that chooses to be taxed as an S-Corporation, you’ll need to pay yourself through a payroll system. OnPay can and does support LLC’s that pay themselves once a year — or weekly. For any specific questions related to setting each of these entities up, talk to your bookkeeper, accountant, or tax professional.

  • Our nonprofit receives some grant funding. Are we able to separate employee pay by grant items using OnPay?

    Yes, it’s possible since you are able to have access to unlimited pay runs per month with OnPay.