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."
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.