Shaun Harvey will depart the Football League at the end of the season after being asked to step down by the board.
Harvey, the chief executive, has been under intense scrutiny following the controversial new £595m TV deal and his future was decided at a board meeting on Monday.
Rebel Championship clubs, including Leeds United, Aston Villa and Derby County, discussed taking drastic action in their battle with Harvey by mounting a legal challenge and a vote of no confidence, after the five-year contract was agreed with Sky Sports in November.
Harvey, 48, had angered clubs by going ahead with the deal, with the EFL later insisting it was agreed in the best interests of the 72 clubs outside the Premier League.
Those clubs insist they were not properly consulted and have communicated their dissatisfaction with Harvey to the governing body.
Harvey will now leave at the end of the season, admitting in a statement he is proud of his five-and-a-half year reign despite operating “in what have not always been easy circumstances”.