Martin was announced as the chief executive last year, replacing longstanding CEO Brian van den Hurk, who retired at the end of 2016.
Officially starting in August last year, Martin has faced a challenging year at the helm.
His departure comes off the back of the agency laying off over 20 staff, following on from client losses at the agency.
Read more: NZ's 'most effective' ad agency axes more than 20 staff - sources
The losses included the Paper Plus account to independent agency Contagion and the VW account to network-owned DDB.
In addition, the agency also faced a loss of business with Noel Leeming taking some of its advertising work in-house.
There has, however, also been good news for FCB this year, with the agency picking up the Samsung and VTNZ accounts from competitors, adding to a stable that includes Pak'nSave, Mercury, Mitre 10 and numerous other major clients.
A number of senior staff have left from the agency in the past 12 months - including FCB managing director Fleur Head, general manager Matt Scott, general manager of retail Kamran Kazalbash and general manager of FCB's media division Rufus Chuter
FCB said it is currently recruiting for a new chief executive.