The charity declined to say whether it now plans to hold a pitch for the business.
The account has delivered some success for JWT in the past. It won a bronze medal in the IPA Effectiveness Awards 2002 for a campaign that used children's stories without happy endings to focus on the idea that every pregnancy should have a happy ending.
Tommy's was the first brand to use escalator advertising in May 2004 at four shopping centres. This outdoor campaign highlighted that many premature babies would not be able to take their first steps.
Jane Brewin, the chief executive for Tommy's, said: "JWT has made an enormous contribution to building up Tommy's brand, and we are extremely grateful."
Alison Burns, the chief executive of JWT London, added: "JWT London is extremely proud of the work it has developed in close partnership with Tommy's over the years, and we wish the charity well."