Military Super chief executive John McCullagh will depart after nearly five years with the fund.
McCullagh is set to retire later this year, and the fund has appointed executive search firm Cordiner King to find a replacement.
McCullagh was hired by Military Super in August 2003 as an interim general manager.
The ex-chief financial officer of the fund's administrator ComSuper immediately began work on obtaining a Financial Services Reform licence from ASIC.
In July 2004 he moved into a permanent role as chief executive with the fund.
Military Super manages $3 billion in funds under management and has unfunded liabilities approaching $12 billion.
In December 2007 an independent report called for an overhaul of the superannuation scheme to meet these unfunded liabilities.