Clarke was earlier forced to apologise after he used the word “coloured” among other controversial comments before a Digital, Culture, Media, Sport committee.
The FA said: “We can confirm that Greg Clarke has stepped down from his role as our chairman.
“Peter McCormick will step into the role as interim FA chairman with immediate effect and the FA Board will begin the process of identifying and appointing a new chair in due course.”
Clarke was criticised by anti-discrimination group Kick It Out after saying that black and South Asian people had “different career interests” from each other, and also drew complaints for saying a coach had told him that the lack of women’s goalkeepers was due to girls not liking the ball being kicked at them.
Stonewall UK was among those who condemned Clarke when he insinuated that being gay was a “life choice”.