The charges relate to the 2022-2023 season, when United were promoted from the Championship (second-tier), and the club were also given a further two points suspended, which will be activated if they default on a payment to another club.
"An independent Disciplinary Commission (IDC) has determined that Sheffield United Football Club are to be deducted two points at the start of the next season the Club is in the EFL’s jurisdiction, with a further two points suspended until the end of that same season," the EFL statement said.
The Premier League's bottom club United said they will not appeal the sanction and have agreed to pay the EFL's costs of 310,455 pounds ($388,565.48).
"The club took the view that it was better to reach an agreement which minimised the risks of a higher deduction or further transfer embargoes being imposed, and being distracted by lengthy and costly legal proceedings," a United statement said.
"The club is now in a position to close this matter and concentrate on the future."
The EFL sent a letter in March 2023 informing the club that they had decided to refer them to a Disciplinary Commission.
United say the relevant sums had been paid in full, on several occasions only days after they were due, or renegotiated with new payment dates adhered to before they were notified of the referral.
The payments defaulted on related to five different player transfers - three permanent transfers and two loan agreements -and were cumulatively in excess of 600 days.
The Blades are currently bottom of the Premier League on 16 points from 31 games, nine points behind Nottingham Forest, who are 17th and in the safety zone having played a game more.
