Walker, who founded the media agency in 1997 with Phil Georgiadis, will leave at the end of June to pursue other interests.
Georgiadis will then take over leadership of the business.
It is likely that Walker's remaining 14% stake in Walker Media will be bought by M&C Saatchi, which currently owns 75% of the agency.
Walker will remain a shareholder of M&C Saatchi plc.
Walker Media is the UK's eighth largest media agency with billings of £252 million in 2006.