Murdoch, son of News Corporation chairman Rupert Murdoch, was appointed as chief executive in November despite fierce shareholder opposition.
The 30-year-old Murdoch Junior won the race to replace Tony Ball beating Stewart, who had been at BSkyB five years and was said to be the City's favoured candidate, and another internal candidate BSkyB chief operating officer Richard Freudenstein.
Other names linked to the job from the outside included Jim Robbins, chief executive of US cable giant Cox Communications, and Michael Dugan, president of EchoStar, the rival satellite broadcaster to News Corp's DirecTV in the States.
In a statement BSkyB said that Stewart is to leave the broadcaster to pursue other interests. He joined BSkyB as group financial controller in 1996 and became chief finance officer in May 1998.
Stewart said that after eight years at Sky it was time to move on but gave no hint of where he might be heading next.
"I have been privileged to work at Sky in a uniquely fascinating phase of its development during which it has evolved from an analogue product to the UK's leading digital platform with over 7m customers. After eight years of service to BSkyB, it is now the right time for me to pursue new opportunities," he said.
He will remain in his post until August unless a new chief finance officer is appointed before that date, in which case BSkyB said Stewart has agreed to assist in the transition process.
James Murdoch said: "Martin has played an enormous role in the success of Sky and has been instrumental in the company's transition from analogue to digital. He will be leaving the company in a superlative position thanks in no small part to his contribution across the operations and strategy of the group."
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