Mr Shine, a former senior executive at Fox News, had been tasked with developing more positive media coverage of the president.
"Assistant to the president and communications director Bill Shine offered his resignation to the president yesterday evening, and the president accepted", White House Press Secretary Sarah Sanders said in a statement.
Trump's campaign manager, Brad Parscale, said that Shine's addition to the re-election campaign will make the campaign "stronger".
The president commended Shine for an "outstanding job" in the administration.
Shine resigned from the United States television network less than a year later over questions concerning his handling of the Ailes case and accusations that he had helped cover up alleged misbehavior. "To be a small part of all this President has done for the American people has truly been an honor".
Shine's resignation came in the same week of an explosive New Yorker report about the cozy relationship between Trump and Fox News.
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Shine did not join Trump on his high-stakes trip to Vietnam for a summit with North Korea's Kim Jong Un.
Shine, a former executive at Fox News, said in a statement that working in the Trump administration had been "the most rewarding experience my life".
Shine said he was looking forward to spending more time with his family. "I have enjoyed working with him and witnessing first hand his unmatched talent, expertise, and skills".
"Bill Shine has been a great leader on our team and someone we have all loved working with every day", Sanders said.
The White House this week refused an official request from the House Oversight Committee. "He has brought a tremendous amount of talent and expertise to the Administration". Others who served in that role were Anthony Scaramucci, who lasted just 11 days, Sean Spicer and Mike Dubke. One source close to the White House told CNN that Trump had questioned Shine's judgment on a number of issues in recent months, from the midterm election to the government shutdown.