Valerie Watts is to return to Northern Ireland where she is to become chief executive of Health and Social Care.
Ms Watts resigned from her position as chief executive of Derry City Council in November 2010 to take up the Aberdeen position.
In a letter to staff, Ms Watts said it had been "a tremendously difficult decision".
She said she had enjoyed her three years in Aberdeen and would remain in post for the next three months.
Barry Black, former chair of Aberdeen City Youth Council, said:"Aberdeen's loss is the young people of Northern Ireland's gain. I wish her all the best."
In June last year, she was asked by councillors to write to senior civil servant, Sir Peter Housden, requesting an inquiry into the First Minister's conduct in making an unannounced visit to a school during the Aberdeen Donside by-election campaign.