Shine's departure was announced Monday. The network said he "resigned."
"This is a significant day for all at Fox News," Rupert Murdoch, the executive chairman of 21st Century Fox, said in a statement announcing Shine's resignation. "Bill has played a huge role in building FOX News to its present position as the nation's biggest and most important cable channel in the history of the industry. His contribution to our channel and our country will resonate for many years."
Shine was one of Roger Ailes' top lieutenants. He was promoted to co-president last summer after Ailes was forced out amid a sexual harassment scandal.
Ever since then, questions have swirled about how much Shine knew about the allegations against Ailes.
Related from last week: Fox News' critics ask: Is Bill Shine the Man Who Knew Too Much?
No one has accused Shine of harassing behavior -- but some ex-employees have charged him with covering up the alleged wrongdoings of others.
Shine has been named in at least four lawsuits or allegations related to alleged sexual harassment or racial discrimination at the network.
That's partly why he was seen as Fox's most vulnerable player, especially after 8 p.m. host Bill O'Reilly parted ways with the network late last month.
The other co-president of Fox News, Jack Abernethy, will remain in that position, Murdoch said Monday afternoon.
Suzanne Scott, currently an executive vice president, will take on some of Shine's duties with a new title, president of programming, overseeing opinion shows like "The Five" and "Hannity."
Jay Wallace will do the same thing on the news side as president of news at Fox News.
Both Scott and Wallace have been with Fox News since its inception -- which means they, too, worked closely with Ailes for two decades.
In a statement, Murdoch praised the pair as "recognized industry leaders" who have "both played a large part in assembling the deepest bench of talented broadcasters and journalists."
Murdoch said "they will lead Fox News to an even more successful future.
-- CNN's Oliver Darcy and Brian Stelter