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Stephen Moir, who is executive director of corporate services, will take up his new role in February.
He has been at the city council since 2017 but also has experience of other senior roles in local government and the National Health Service.
He worked as chief people officer at NHS England and deputy chief executive at the Yorkshire Ambulance Service NHS Trust.
And he had a previous spell working for Cambridgeshire County Council at director level between 2005-2011, and was a national adviser for the Local Government Association.
Council leader Adam McVey congratulated Mr Moir on his appointment. He said: “I know he’ll make a first-class chief executive.
“Stephen joined the council around the same time as I became Leader back in 2017 and I’m extremely grateful for his hard work and support over the last four-and-a-half years.
“His commitment to developing and improving the work of council teams has put the council – and the city – in a far stronger place to deliver more effective services for the people of Edinburgh.
“I know he’s well respected across all political groups and I’m sure all councillors and other colleagues will join me in wishing Stephen well when he leaves us in the new year to take up this new and exciting opportunity.”
Depute leader Cammy Day added: “Stephen has led the way on the development of our ambitious Digital and Smart City Strategy, having transformed the relationship with our IT provider into a far more positive and productive partnership.
“He has also worked closely and constructively with our trade unions throughout his time with us and he’s always championed the key contribution of all our workers across the council. I wish him all the best in his new role.”