US Soccer President Carlos Cordeiro apologised for language in a court filing made by the federation in a legal dispute with its women's national team over pay equity.
The filing said men's national team players had a greater level of responsibility than the women and that their job "requires a higher level of skill based on speed and strength".
The language sparked outrage and prompted an on-field protest by players, while sponsor Coca-Cola told the Wall Street Journal it found the language used in the filing "unacceptable and offensive."
"I sincerely apologise for the offence and pain caused by language in this week's court filing, which did not reflect the values of our federation," Cordeiro said in a written statement.
"Even as we continue to defend the Federation in court, we are making immediate changes.
"I have made it clear to our legal team that even as we debate facts and figures in the course of this case, we must do so with the utmost respect."
The women's team sued the US Soccer Federation for gender discrimination just over a year ago in a lawsuit that included complaints about wages and working conditions.
A trial date has been set for 5 May after talks between the two parties broke down.
On Wednesday, members of the US women's' team took the field for their third and final SheBelieves Cup game against Japan with their warm-up jerseys worn inside out to obscure the US Soccer logo in protest.
After the match, which the United States won 3-1, co-captain Megan Rapinoe said the language in the court filing reflected "blatant misogyny and sexism."
"Their argument keeps changing, ours has stayed the same," said Rapinoe.