After days of speculation that the days of Mr Shine - long seen as a close ally of former CEO Robert Ailes - were coming to an end, the network said he had resigned.
The departure of Mr Shine follows the ousting last month of leading anchor Bill O’Reilly, and the firing of Mr Ailes last year. Both Mr Ailes and Mr O’Reilly had been accused of sexual harassment, allegations they both denied.
Didn't Hannity say that if Bill Shine is pushed out it's the end of Fox News?— Joy Reid (@JoyAnnReid) May 1, 2017
Mr Shine's co-president, Jack Abernethy, will remain. Fox said on Monday that it was also promoted two other executives, Suzanne Scott and Jay Wallace.
Mr Shine had been with Fox News since its inception over 20 years ago.
Last month, Julie Roginsky, a Democratic political consultant and Fox News contributor, sued the network and its former chairman, Mr Ailes, accusing them of denying her a permanent hosting job after she rebuffed Mr Ailes' sexual advances.
At the time, she also sued Mr Shine, asserting that he failed to investigate her claims. Reuters said that last August, Mr Shine and Mr Abernethy were appointed as co-presidents to lead Fox News after Mr Ailes resigned amid the sexual harassment allegations.
In a statement, Fox founder Rupert Murdoch, said: “This is a significant day for all at Fox News. 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.”
In an email to staff, Mr Murdoch suggested he regretted Mr Shine's departure.
“Sadly, Bill Shine resigned today,” Mr Murdoch said. “I know Bill was respected and liked by everybody at Fox News. We will all miss him.”
Last month, Fox’s parent company, 21st Century Fox, announced that was it cutting ties with Mr O’Reilly, who was paid $18m a year.
In an email to staff, the company said the broadcaster, who had for two decades pitched himself as the no-nonsense know-it-all, was leaving following a review of those accusations.
“After a thorough review of the allegations against him, the company and Bill O’Reilly have agreed that Mr O’Reilly will not return to the Fox News Channel,” it said.
Mr O'Reilly said in a statement it was “tremendously disheartening that we part ways due to completely unfounded claims”.