Confirmation of his departure was posted on the BBC website and follows internal issues that led to a meeting between the NUJ and BBC management.
The NUJ raised concerns and threatened to ballot BBC Scotland journalists on taking industrial action.
Mr Boothman, who has headed news operations since June 2011, will be replaced by interim head Peter MacRae.
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.”