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Non Profit

Nonprofit & Tax-Exempt Payroll

Achieve your mission, leave payroll to the experts

Nonprofit payroll has unique requirements. As the online payroll leader backed by our parent company, Paychex, you can depend on RunPayroll to securely and accurately handle your payroll tax work. Your satisfaction is 100% guaranteed.

Running Nonprofit Payroll Yourself
  • You’ll need to keep up with rules under IRS Section 501(c)(3). 
  • Withhold the appropriate payroll taxes each pay period.
  • Deposit and report tax filings including Form 940 and 941 along with federal, state and local taxes.
  • Keep up with the changing IRS payroll tax regulations.
With RunPayroll You Get
  • Automatic tax pay & file of your federal, state and local payroll taxes, plus your W-2s posted online at year-end.
  • Direct deposit or print checks yourself.
  • Affordable payroll, at up to half the cost of traditional payroll services.
Get an Instant Payroll Quote

Get Started With Your First Payroll FREE!


Nonprofits nationwide use RunPayroll to provide comprehensive payroll tailored to their unique needs. You’ll get free setup with the help of one of our payroll experts, a free walkthrough on how to use our easy online service and an affordable price that beats traditional services.