The departure is a blow to the agency, which, following its acquisition by the Publicis Groupe and subsequent merger with D'Arcy, was relaunched a year ago under its new group chief executive, Bruce Haines.
Haines said: "Paul and Jim have worked hard to build a working relationship that was right for the two of them, for the agency and for our clients.
"Unfortunately, after a period of six months, Paul has decided that working as a double act is not for him. Paul is an outstanding creative talent and we will miss his contribution. I am sure that he is destined for great things in the future."
The appointment of the creative duo last May was seen as something of a coup and the pair were heralded as the talent to lead the return of Leo Burnett to its former creative glory.
The pair were appointed to replace Nick Bell, who left to join J. Walter Thompson last February. Burnett poached Shearer from Wieden & Kennedy Amsterdam, while Thornton joined the agency from Mother.
Thornton will continue to head the creative department, working alongside the senior management team of Haines, the managing director, Barry Cook, and the planning director, John Poorta.
Haines added: "Jim recognises the tremendous potential here at Leo Burnett and I am proud to have him as our creative director and management partner."
Previously, Shearer had worked at Butterfield Day DeVito Hockney, where he began his career in 1988, working on accounts including BT and Honda.
He also worked at Simons Palmer Denton Clemmow Johnson, Bartle Bogle Hegarty and the then Euro RSCG Wnek Gosper, where he was made the deputy creative director in 1998.
While at W&K, where he worked for three years, Shearer was in sole control of the creative department.
Throughout his career, Shearer has collected various awards including eight D&AD Pencils and two Cannes Lions. At W&K and Simons Palmer, he worked on the Nike account, while at BBH he created Levi's "Kevin the hamster" and Audi "golf club".
Shearer and Thornton took up their positions in the summer of last year.
However, their appointment has not made a significant impact on the agency's reel to date.
Both Shearer and Thornton declined to comment on the story.