Barry Blamire has worked for the firm for 16 years after joining as a graduate trainee. He will succeed Barry Matheson, who is moving to a new role with the company in London.
Mr Blamire was previously managing director of John Lewis Newcastle and will be responsible for heading up all aspects of store operations.
He said: “Working for John Lewis has been hugely rewarding and I’m looking forward to the new opportunity in Edinburgh. It’s a wonderful city.”