Thompson, a former head of television at the BBC, was seen by many as the favourite for the job, but his intention to stay at Channel 4 makes an internal appointment at the BBC more likely.
Mark Byford, the acting director-general, and Jana Bennett, the BBC's head of TV, are seen as front runners.
Speaking as he announced Channel 4's annual results, Thompson said he was committed to staying at the broadcaster to see it through the next stage of its development.
Channel 4 has been considering possible changes to its current funding model following the consolidation of ITV and Ofcom's ongoing review of public service broadcasting.
Luke Johnson, the new chairman of Channel 4, said privatisation of the broadcaster would destroy its remit. Channel 4 had held merger discussions with five but these came to nothing.
Channel 4's pre-tax profits rose from £19 million in 2002 to £45 million.
Turnover was £779 million, up £6 million on the previous year. The improved profits followed cost savings and the first profit from Channel 4's commercial arm, 4 Ventures.