Not all IRS forms are eligible for payment by credit card or debit card, and there are limits on how often you can make payments. If you need to make a payment of $100,000 or more, you might have to coordinate the payment with your bank or credit card company. How to Pay Payroll Taxes to the IRS Posted by The Law Offices of Nick Nemeth on October 20, 2016 By definition, payroll taxes are taxes imposed on employers or employees, and are usually calculated as a percentage of the salaries that employers pay their staff. Step 1: Complete an IRS Form 941, Employer's Quarterly Income Tax Return, or annually Form 943 for Agriculture Employees. The main purpose of the form is to report the wages you pay, the tips your employees earn and to calculate the amount of federal income tax, Social Security tax and Medicare taxes you should have withheld and owe to the IRS.