Harvey has been CEO of the body, which governs the three professional divisions below the Premier League, since 2013.
"After discussions with the Board, we decided that the time is right for the EFL to now move in a different direction having concluded a number of commercial contracts that leave the League in a stable position," Harvey said in the statement.
Debbie Jevans, Interim Chair of the EFL said: "The EFL would like to thank Shaun for all he has delivered since joining as CEO in 2013. The EFL is in a strong position with a growing fan base throughout the world and Shaun deserves a lot of credit for this."
"Shaun and the Board have agreed that the time is now right for a change of leadership and a new direction. We are pleased that Shaun has agreed to stay on until the end of the season," she added.
The Premier League is also currently looking for a new CEO to replace Richard Scudamore who stood down in December.
(Reporting by Simon Evans; Editing by Christian Radnedge)
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