Her departure, described by the agency as "mutual", is understood to be connected with moves to introduce more flexibility into the agency's creative department.
Chris Herd, the managing director of Bates, said: "Pat is a terrific creative and we part as friends." There are no immediate plans to replace her.
Doherty, a former Bartle Bogle Hegarty creative director, was signed by Bates in June 2001, along with Rob Kitchen, the former CDP creative chief.
The pair were the first major hirings to be made by Andrew Cracknell since his return to Bates as its executive creative director. Their arrival was in line with his declared aim of getting more "grown-ups" into his department and of strengthening its second-tier management.
Doherty, a copywriter, is best known for her work on the Saatchi & Saatchi BT commercial starring Stephen Hawking, as well as the "lifeboat" spot for Alka-Seltzer, which won a gold at Cannes for Abbott Mead Vickers BBDO.
She joined Bates from the Big Green Door branding consultancy.
Bates is introducing what it says is a more modern method of working in its creative department, involving creatives working more closely with clients rather than in isolation.
"We want to mould our creative resource to meet the needs of individual clients," Herd explained. "I think that both we and Pat realised that we were heading in different directions."