Keith Lamb, a science teacher, claims the professional body, set up by Labour in 2000, is a waste of money. His school, Bishop of Winchester comprehensive decided it had no option but to end his contract.
Mr Lamb, who is considering legal action, said: "We have teacher unions and the Government already had a register of people's qualifications, so I don't see any need for the GTC."
Jean McBain, head at Bishop of Winchester, said: "I respect Keith's right to stand by his principles. Nevertheless registering with the GTC is a legal requirement and despite the support and guidance of colleagues, governors and his professional association, Keith has decided to maintain his stance resulting in the loss of his job."
A GTC spokeswoman said she thought that Mr Lamb must have originally been registered automatically as a supply teacher, despite never paying a pound;30 fee. After failing to respond to letters from the GTC he was removed from the register in April 2004.
The former army physical training instructor is confident he will find another job. He has taught PE and key skills in schools and is a qualified joiner, lifeguard, canoe, ski and rock-climbing instructor. He says he has had offers from private schools where GTC membership is not compulsory.
The GTC criticised ministers this week when it was revealed that teachers in academies would not have to be registered.