The Radio 4 Journalist, who has been drafted in to head up the show during the independence referendum campaign, presented the show for the first time today.
Mr Naughtie, from Aberdeenshire, will present the programme two days a week while also working for Radio 4's Today.
The broadcaster will also act as a chief reporter for Radio 4's coverage of the run-up to the vote next year. The BBC has said he will have "an enhanced role" in the BBC's independence referendum team.
The Scot has been has been a presenter of the Today programme since February 1994, and before that worked in a variety of newspapers.
Educated at Aberdeen University and Syracuse University, New York, Mr Naughtie began his career at the Aberdeen Press & Journal in 1975 before moving to the Scotsman, subsequently becoming the paper's chief political correspondent.
In 1981 he worked on the national staff of The Washington Post as the Laurence Sterne Fellow and joined The Guardian in 1984, becoming its chief political correspondent in 1985, before moving over to broadcasting.
The opera buff has presented programmes on classical music and currently chairs Radio 4's Bookclub programme, recently interviewing Man Booker Prize-winning author Hilary Mantel.
However, his career has not been without controversy. Earlier he told two guests on the Today programme to "shut up, just for a second". The Today presenter intervened as Times columnist Jenni Russell and Sunny Hundal, who runs the Liberal Conspiracy site, got in a spat over Ed Miliband's performance record.
When Mr Naughtie's new role was announced, BBC Scotland director Ken MacQuarrie said: "The referendum story is of huge significance for BBC Scotland and I'm delighted James will be contributing to our coverage of it as part of the Good Morning Scotland presenting team."
Mr Naughtie said: "The constitutional debate and the decision next year have great historic importance for Scotland and the whole of the UK, so I am excited to be in the thick of it, on both sides of the Border, from start to finish.
"The opportunity to spend more time in Scotland in referendum year is something I am looking forward to immensely."