The short answer
Paycom quotes every client and runs HR and payroll on one database, with employees approving their own paychecks before each run. Paychex Flex publishes Flex Essentials at $39 a month plus $5 per employee for businesses under 20 workers and quotes its larger packages.
LeadChange Score: editorial assessment based on public information.
Paycom wins 1Paychex Flex wins 21 tie
| Dimension | Paycom | Paychex Flex |
|---|---|---|
| PricingPaychex Flex lists Flex Essentials at $39 a month plus $5 per employee. Paycom quotes a Core set per suite plus Complete tools and a one-time implementation fee. $39/mo | Quote only | $39/mo + $5/employee/mo |
| IntegrationsPaychex Flex offers a REST API with webhooks and lists QuickBooks, Sage Intacct, Xero and NetSuite among its integrations. Paycom sends general ledger reports for direct import and enrollment feeds to benefit carriers. REST | 0 documented | 15 documented |
| Fit and supportPaycom assigns a dedicated specialist and live operators; Paychex lists 24/7 payroll support by phone, chat and email. Dedicated specialist, Live operators, Help Center | Small businesses, mid-market companies, enterprises | Small businesses, mid-market companies |
| SecurityPaycom lists five ISO certifications, including 27001, and supports SAML 2.0 single sign-on. Paychex names no certification on the Flex pages we reviewed. Yes | ISO 27001 | None verified |
| Attribute | Paycom | Paychex Flex |
|---|---|---|
| Pricing model | Quote only | Base fee + per employee |
| Price transparency | Quote only | Partly published |
| Best for | Small businesses, mid-market companies, enterprises | Small businesses, mid-market companies |
| Deployment | Cloud | Cloud, mobile |
| Support channels | Dedicated specialist, Live operators, Help Center | Phone, chat, email, in-platform help center |
| Typical implementation | Most organizations are implemented within three months | Self-guided online setup; first payroll as soon as the same day |
| Founded | 1998 | 1971 |
| Headquarters | Oklahoma City, Oklahoma | Rochester, New York and Cincinnati, Ohio, US (dual headquarters) |
| Attribute | Paycom | Paychex Flex |
|---|---|---|
| Mobile apps | Paychex Flex app (iOS), Paychex Flex app (Android), Paychex Flex Time Kiosk app | |
| Automatic tax filing | ||
| Ownership | Publicly traded | Publicly traded |
Pricing. Paychex Flex lists Flex Essentials at $39 a month plus $5 per employee. Paycom quotes a Core set per suite plus Complete tools and a one-time implementation fee.
Capabilities. Both cover payroll, time, HR and benefits. Paycom adds talent acquisition and talent management suites, employee-run paycheck checks and daily pay.
Integrations. Paychex Flex offers a REST API with webhooks and lists QuickBooks, Sage Intacct, Xero and NetSuite among its integrations. Paycom sends general ledger reports for direct import and enrollment feeds to benefit carriers.
Fit and support. Paycom assigns a dedicated specialist and live operators; Paychex lists 24/7 payroll support by phone, chat and email.
Security. Paycom lists five ISO certifications, including 27001, and supports SAML 2.0 single sign-on. Paychex names no certification on the Flex pages we reviewed.
Patriot Payroll has the highest LeadChange Score in Payroll Software after excluding these two (9.3/10).
From $17/mo + $4/employee/mo
No. Paycom is a public company founded in 1998 in Oklahoma City. Paychex, founded in 1971, has dual headquarters in Rochester, New York and Cincinnati, Ohio, and sells Paychex Flex.
Yes. Paycom files payroll taxes for its clients; Paychex Flex calculates, files and pays payroll taxes through Taxpay and handles multi-state compliance. On Flex Essentials, tax administration may carry extra fees.
Both list small businesses among the sizes they serve. Paychex Flex publishes a price for teams under 20 and starts the same day; Paycom quotes and implements most clients within three months.
Paychex Flex Essentials costs $39 a month plus $5 per employee, $89 a month for 10 employees. Paycom quotes every client, with a one-time implementation fee in the quote.
Yes, with both. Paycom’s Beti lets employees review, fix and approve their own paychecks; Paychex Pre-check lets employees review their paycheck before payroll is processed.
Paycom’s IWant searches employee, applicant and policy data by command, and GONE decides time-off requests from rules you set. Paychex flags payroll issues before they cause delays and generates HR documents.
Only Paycom states ISO 27001.
Paycom ranks #9 of 12 in our payroll software ranking. Besides Paychex Flex, the highest-scored are Patriot Payroll, QuickBooks Payroll, and Gusto. Every alternative, matched to the reason you might switch: Paycom alternatives.
Your team size, what matters most and your role: see which one fits more of your answers, from verified facts and list prices. Then, if you like, ask to hear from both.
LeadChange may earn a fee when you request pricing through our site or follow a sponsored link. Rankings never depend on whether a vendor pays us.We may earn a fee.
How we make money
LeadChange may earn a fee when you request pricing through our site or follow a sponsored link. Rankings never depend on whether a vendor pays us.
What the LeadChange Score means
A 0–10 editorial assessment built only from verified facts, across six weighted dimensions: capabilities, pricing, integrations, security, fit and support, and data confidence.
Payments, commissions and lead fees are never inputs.
