Confirmation of his departure was made in an email to staff on Tuesday.
The 57-year-old, who has headed news operations since June 2011, will be replaced by interim head Peter MacRae.
Mr Boothman has been with the BBC for 30 years and recently oversaw general election and Scottish independence referendum coverage.
In an email to staff, BBC Scotland Director Ken McQuarrie said: "We are now entering the most important period of work ahead of the forthcoming Charter Review discussions as we shape our plans for the future of BBC Scotland.
"I am writing to let you know that John Boothman, Head of News and Current Affairs will be joining the team working on Scotland's proposals for Charter Review.
"Working to Bruce Malcolm, he will play a key role focusing on service development for Scotland including our news offer for audiences for the new Charter period.
"Pete MacRae will take on the role of Head of News and Current Affairs on an interim basis until a permanent appointment is made."

Mr Pompeo said he was "honoured and humbled" to accept US President-elect Donald Trump's job offer as Central Intelligence Agency director.
The 52-year-old, a three-term tea party Republican from Wichita, Kansas, is a vehement critic of the Obama administration's nuclear deal with Iran.
He has also defended the National Security Agency's bulk data collection programme and opposes shutting the prison at Guantanamo Bay.
After visiting the detention facility in 2013, he remarked that some inmates who had declared a hunger strike looked like they had put on weight.
Mr Pompeo also defended the CIA after the 2014 release of the Senate Intelligence Committee Report on Torture, which detailed such interrogation practices as waterboarding.
He declared: "These men and women are not torturers, they are patriots".
The CIA tactics, he declared, "were within the law, within the constitution".
Mr Pompeo graduated first in his class at West Point and graduated from Harvard Law School, where he was an editor of its Law Review.
He was elected to the House of Representatives in 2010 with the support of the Republican mega-donors Charles and David Koch.
Mr Pompeo became a member of the House Select Committee on Intelligence and the House Energy and Commerce Committee.
Before joining Congress, Mr Pompeo founded an aviation parts firm and an oilfield supply company.
He was accused of Islamophobia for remarks he made following the deadly 2013 Boston marathon bombing.
Mr Pompeo took to the House floor to suggest some Islamic faith leaders might be tacitly encouraging terrorist attacks.
"When the most devastating terrorist attacks on America in the last 20 years come overwhelmingly from people of a single faith and are performed in the name of that faith a special obligation falls on those that are the leaders of that faith," he said.
"Instead of responding, silence has made these Islamic leaders across America potentially complicit in these acts and, more importantly still, in those that may well follow."
While he was a congressional candidate in 2010, one of his campaign aides sent a tweet linking to an article that labelled his Indian-American Democratic opponent Raj Goyle a "turban topper".
Mr Pompeo apologised; his campaign also sent out billboard ads urging everyone to "vote American".
He also served on the House Select Benghazi Committee, a special panel created in 2014 to investigate the deadly attack two years earlier on a US diplomatic compound in Libya.
Democrats described it as a political witch hunt against former Secretary of State Hillary Clinton.
Mr Pompeo released a report afterwards accusing her of intentionally misleading Americans about the nature of the attack to help President Barack Obama's re-election bid.
John Boothman is to leave his position as BBC Scotland's head of news and current affairs to work on the corporation's Charter renewal bid.
[NEXT_CONCEPT]
The United States' likely new spymaster, Mike Pompeo, is a hardline Republican Congressman and a national security hawk with a background in military and intelligence affairs.