There are 2 choices.
The IRS has a free payment system (electronic payment from your bank account) on their website called Direct Pay, but it does not allow you to schedule recurring payments. You'd have to enter it each quarter. You can schedule a payment up to 30 days in advance. There is a FAQ section there.
https://www.irs.gov/payments/direct-pay
Or you can set up an account at the Treasury's EFTPS and schedule recurring quarterly payments in advance out of your bank account, also with no fee.
The
Treasury offers the free EFTPS (Electronic Federal Tax Payment
System). You can make 1040-ES payments electronically, as well as other
Federal tax payments including balances due on your annual Form 1040,
etc. You have to set it up in advance with your banking info at the
website. Once you enroll and they verify your info, the Treasury will
send you a PIN in the mail, which you use each time you make a
payment. The payment is then debited from your bank account. You can
set up multiple payments in advance, or even make extra payments. Once
you set it up, you can even make tax payments by phone, and you don't
have to mail in any paper 1040-ES forms. You can print out
confirmations or download the confirmation as a PDF. Read more at the
sites below.
There is an extensive FAQ at: https://www.eftps.gov/
Also see this article:
http://www.irs.gov/uac/EFTPS-The-Electronic-Federal-Tax-Payment-System
