Gilson has edited The News since 2000 and has been a member of the Press Complaints Commission's code committee for three years.
Prior to joining The Scotsman, he was editor of The Peterborough Evening Telegraph, night editor of The Western Mail, and news editor of the Hull Daily Mail.
Gilson said: "Any newspaper I edit places itself at the centre of debate, sparks opinion and is talked about. The Scotsman I edit will tackle the issues of the day, addressing the concerns of its readership and the community as a whole."
The news comes after Johnston Press, owner of The Scotsman, announced that Les Snowdon was to become editor of Scotland on Sunday, after holding the position at Sunday Times Scotland.
Michael Johnston, managing director of Johnston Press' Scottish division, said: "Mike Gilson and Les Snowdon are two outstanding journalists. Their appointments underscore Johnston Press' commitment to The Scotsman and Scotland on Sunday's future as the nation's leading quality newspapers."
The Scotsman sank below 60,000 in the latest ABC figures, with Scotland on Sunday falling 6.54% to 67,049.
It has been a tough year for many Scottish newspapers, with The Herald falling below 70,000, Johnston Press' Edinburgh Evening News falling 7.5% year-on-year, and Newsquest's Glasgow Evening Times hovering just above 80,000.
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