It is understood that Professor Paine strongly disagreed with Sir Cyril Taylor, the trust's chairman, about the future direction of the organisation. He will leave in December, after the trust's annual conference.
He said: "It was my decision, but I just felt the best thing I could do was move on. Sir Cyril agreed it was the right decision and he's been very supportive," he said.
His announcement - and the fact that he is not leaving to take up another role - has surprised many in the sector.
Professor Paine successfully ran the Scottish Coucil for Educational Technology for nine years before accepting Sir Cyril's invitation to head the trust last year.
Since the 1997 election, Sir Cyril, formerly a Conservative favourite, has become an adviser to David Blunkett, the Education Secretary, on specialist schools.
All specialist schools can affiliate with the Technology Colleges Trust and more than 850 have done so. The schools receive about 4 per cent more funding than comprehensives and have achieved much better results according to York University research released earlier this year.
See next week's TES Online magazine for an interview with Nigel Paine. The Technology Colleges Trust website is at www.tctrust.org.uk