Paychex offers three pricing plans, with the most basic one, Paychex Flex Essentials, costing $39 per month plus $5 per employee. This includes payroll processing, payroll tax administration and general ledger features. Paychex customizes its prices for its other two plans, Paychex Flex Select and Paychex Flex Pro, so you'll need to contact the company for a personalized quote.