He leaves the station at the end of January without a job to go to, although is expected to make an announcement about his future next month.
Woodward's departure has prompted speculation that the Channel 4 commercial department, 4Ventures, will be restructured in the New Year.
Woodward was in charge of Channel 4's business affairs and finance teams as well as the FilmFour channels, E4, Channel 4 International, 4 Interactive and the consumer products department.
Andy Duncan, chief executive of Channel 4, said: "In his three years at Channel 4, Rob worked hard to develop a commercial agenda for Channel 4 alongside its public service remit. In addition, he's done a great job in organising a set of disparate businesses into a coherent and well-managed whole under the 4Ventures banner.
"The improvement in the 4Venture's bottom line is testament to his achievements over the last three years, with a £60m loss turned into significantly increased profits this year."
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