The veteran journalist has presented Radio 4's flagship breakfast news programme for more than 21 years.
He is also being appointed BBC News Books Editor and will present a book review on Radio 4 on Saturday mornings.
BBC director general Tony Hall called Naughtie "the emotional heart of Today for a generation".
Naughtie joined Today in 1994 following the death of Brian Redhead, having spent six years as presenter of The World at One.
He has anchored every election results programme for BBC Radio since 1997 and has worked on every US presidential election since 1988.
Last year, he become a chief reporter in the BBC's coverage of the independence referendum in Scotland.
In recent years, he has written and presented radio documentaries including a 60-part story of classical music, The Making of Music.
His new role as Books Editor comes as a result of presenting Radio 4's monthly Bookclub since it began in 1998.
The 63-year-old said: "It was exciting to discover that the BBC and I had the same idea about what I should do next. I'm thrilled to be moving from one dream job to another, and working with the programmes across Radio 4 - including Today - that I love and have known for so long.
He added: "After 21 years, I can turn off that 3am alarm at last".
Presenter James Naughtie is to leave Radio 4's Today programme and take on a new role as a special correspondent from early next year.