George Bodenheimer will be the sports network's acting chairman for the next 90 days, ESPN said in a statement. He had been its president from 1998 to 2011 and executive chairman until May 2014.
An ESPN spokeswoman declined to comment on who may be considered as Skipper's successor.
Skipper's departure comes within a few days after Disney struck a deal to buy film, television and international businesses from Rupert Murdoch's Twenty-First Century Fox Inc for $52.4 billion.
Skipper, who became ESPN president in 2012, has led the network to a series of long-term distribution agreements with major rights holders, including the National Basketball Association and Major League Baseball.
But ESPN has also struggled with subscriber losses and ratings declines. Last month, it said it would lay off about 150 employees.
Disney Chief Executive Officer Bob Iger, who extended his stay at the company through 2021 to oversee integration of Fox's businesses, lauded Skipper's candor and backed his decision.
Disney shares were down 0.2 percent at $111.09 on Monday afternoon.
(Reporting by Aishwarya Venugopal in Bengaluru and Sheila Dang in New York; Editing by Arun Koyyur and Lisa Von Ahn)
