Best Payroll for Nonprofits 2026
Nonprofits need affordable payroll that handles tax-exempt status, grant-funded positions, and compliance with nonprofit regulations.
🏆 Top Pick
Gusto
$40+$6/personNonprofit-friendly with transparent pricing. Handles tax-exempt payroll, multiple funding sources, and worker classification. No hidden fees.
Transparent pricingTax-exempt supportMultiple funding$40+$6/personEasy interface
Visit Gusto →🥈 Runner Up
OnPay
$40+$6/personSimple nonprofit payroll. Same transparent pricing with simpler interface. 1-month free trial to test before committing nonprofit budget.
$40+$6/personFree trialSimpleTax-exemptNo add-ons
Visit OnPay →💡 Also Great
Not sure? Take the full HR & Payroll Software quiz for a personalized pick →
Paychex
CustomNonprofit discounts available. Paychex offers nonprofit pricing on request. Dedicated specialist understands nonprofit payroll requirements.
Nonprofit pricingDedicated specialistCustom quoteComplianceScalable
Visit Paychex →Affiliate Disclosure: Some links are affiliate links. We may earn a commission at no extra cost to you. All pricing reflects current publicly available rates. Our quiz results are determined by the scoring engine, not by commission rates. Learn how our scoring works.