Scott is responsible for the company's finance, IT, legal and compliance and operations functions and is Channel 4's managing director.
He joined Channel 4 18 months before it launched in November 1982 but is stepping down in autumn 2005 to pursue other interests.
His departure is the first major management change since Andy Duncan became the chief executive of the channel in June.
Scott was one of only five executive directors on the Channel 4 board - the Government exerts its control by imposing a majority of non-executive directors - and an internal appointment will have to replace him.
Scott is relinquishing his management responsibilities for Channel 4's finances with immediate effect to Sue Ford, the director of finance, but will continue to represent Channel 4 on industry groups, including the digital switchover group SwitchCo; on the BBC Charter Review; and Ofcom's review of Public Service Broadcasting.
Scott said: "Channel 4's programmes and finances are in excellent shape. In the next 12 months, the key issues governing the channel's future status and funding will be decided and now is a natural junction to plan to step aside. Andy is planning now for the channel's long-term future and I wanted to give him adequate warning that I do not intend to be part of those plans."
Duncan added: "David has been absolutely instrumental in building the strong financial and business foundations on which Channel 4's fantastic track record of creative innovation has been based."