Magnus Llewellin, who is currently the paper's deputy editor, takes on the new role with immediate effect.
Mr Llewellin, 47, began his career in Scotland 22 years ago with the Edinburgh Evening News and, prior to joining The Herald, he worked at the Daily Record, The Scotsman and Business AM.
He said: "I am delighted to take on what I regard to be the best job in Scottish journalism at such an important time in this nation's history."
Married with two young daughters, Mr Llewellin chairs the judging panel of the Scottish Politician of the Year Awards and is a committee member of the Journalists' Charity in Scotland.
A keen sports fan, his hobbies also include hillwalking, running and travel.