A foundation can pay the taxes using the Electronic Federal Tax Payment System (EFTPS) or Electronic Funds Withdrawal (EFW).
To pay taxes through EFTPS, it's your responsibility to visit their portal www.EFTPS.gov to make the payment. Payments made through EFTPS should generally be made one day before the tax payment due date for the transactions to happen on time. For more information about EFTPS or to enroll in EFTPS, visit the EFTPS website at EFTPS.gov, or call 800-555-4477.
To pay taxes through EFW, you have to provide your checking or savings account information for the IRS to withdraw money from your account based on the Payment Request Date you choose.
Small Foundations can also pay their section 4940 taxes through check or money order to the United States Treasury along with the Form 990-PF or the extension form.