McClendon will step down even though Chesapeake says a review of his business dealings has not revealed improper conduct.
Chesapeake Chairman Archie Dunham said in a statement the company needs a new leader to help develop the oil and gas assets the company has amassed under McClendon.
McClendon, 53, founded the company 24 years ago and pushed it to acquire drilling rights to huge amounts of land.
The strategy landed the company promising assets — and enormous debt.
A plan that allowed McClendon to invest personally in the company's wells came under renewed scrutiny last year, and he was forced to step aside as board chairman.
Chesapeake shares rose 9 per cent in after-hours trading.