Harris, who helped found the direct and digital M&C Saatchi off-shoot in 2000, is departing to pursue his own entrepreneurial interests.
Harris set up the agency alongside the chief executive, Lisa Thomas. The agency's clients include British Airways, NatWest, the RAF and Mini.
Thomas said: "David has been instrumental in expanding the agency and his unique multi-disciplinary experience has been fundamental to the success of Lida."
Although Harris was not specific about his plans, there is some speculation that he is plotting another start-up. Harris said: "After taking two months off, I'd like to do something that will maximise all the changes in the industry at the moment. I am sad to leave an agency I have seen flourish over the past years."
Thomas said Harris will be replaced, but could not name his successor.
Moray MacLennan, the chairman of M&C Saatchi Europe, said: "Harris' advertising pedigree, and his direct and digital experience, has made a huge contribution not only to Lida, but to the whole M&C Saatchi Group."
In the absence of Harris and Thomas, who is on maternity leave, the agency will be run by the creative partner, Peter West, and the creative group head, Nicky Ballard.