Valerie Watts is to return to Northern Ireland, where she worked previously, to take up a job with the Northern Ireland Government.
The former chief executive of Derry City Council, who has been at Aberdeen only three years, is thought to be heading to the Stormont administration's health and social care department.
She said in a statement released tonight: "It is with truly mixed feelings that I write to let you know that I have today met with the council leader to tell him that I have accepted the appointment as chief executive of Health and Social Care Northern Ireland based in Belfast.
"As a result I have given him notice of my intention to leave the city council.
"This was a tremendously difficult decision that took me some time to make. In the end I could not resist the opportunity to take on the fresh challenge of such a demanding role, improving the wellbeing outcomes for all the people of Northern Ireland.
"However, I have greatly enjoyed my three years in Aberdeen and I know that I am going to miss the Council and the city."
Barry Black, former Chair of Aberdeen City Youth Council, said: "Valerie arrived at a difficult time when the last SNP-Liberal administration had cut youth projects across the board in Aberdeen and was always eager to fight for those who had been worst affected."