England and Wales Cricket Board chief executive Tom Harrison will step down in June.
Harrison was appointed in 2014 and oversaw the introduction of The Hundred, which started last year.
Former England captain and women's cricket managing director Clare Connor will take over on an interim basis.
Harrison's departure continues an extensive overhaul in England men's cricket after the heavy Ashes defeat in Australia over the winter.
Brendon McCullum has taken over as men's Test coach, with Ben Stokes replacing Joe Root as Test captain and Rob Key appointed managing director.
Key replaced Andrew Strauss, who had stepped in on an interim basis after Ashley Giles' departure in February, the day before Chris Silverwood left his position as coach.
Root resigned in April following England's 1-0 defeat in the West Indies, which left the side winless in nine Tests and with only one win from their past 17 matches.
During Harrison's tenure, England won both the men's and women's 50-over World Cups.
The England and Wales Cricket Board (ECB) is still searching for a new chairman following the departure of Ian Watmore in October.
Interim chair Barry O'Brien stepped down because of ill health last month, handing over to deputy chair Martin Darlow.
More to follow.