Peter Peace, once an assistant head at the Royal High, was dismissed by Edinburgh City Council after being found between 1991 and 1994 to have formed inappropriate relationships with pupils. The case was referred to the GTC and Mr Peace was subsequently struck off the register.
Mr Peace challenged the employment practice of his local authority but lost his appeal last April. He has now overturned the decision of the GTC disciplinary committee in a judgment that adds further embarrassment to the gatekeeper of the profession.
He is the second teacher to win a procedures battle against the GTC after a North Lanarkshire father won his appeal in the Court of Session in November 2001. The teacher was removed for "conduct infamous in a professional sense" after a court found him guilty of assaulting his eight-year-old daughter in a dentist's surgery.
Mr Peace faced similar "infamous conduct" charges but three of Scotland's senior judges - Lords Marnoch, MacLean and McCluskey - have unanimously condemned the GTC's practices when it heard the case in the autumn of 2001.
It failed to comply with regulations in finding Mr Peace guilty and striking him off.
Lord McCluskey concludes that the disciplinary committee gave no reasons or explanations for any of its decisions and proceeded "upon the basis that a nod is as good as a wink". He describes the committee's thinking as "inscrutable".
He comments: "The reasoning process of the disciplinary committee is not revealed; and the bare facts do not support a finding of guilt of infamous conduct."
The GTC this week offered a strict "no comment" while it studies the scathing judgment but procedures have been tightened since the previous Court of Session setback in 2001. The disciplinary committee is now advised by a QC.
A spokeswoman for the city council said the matter was "closed" as far as it was concerned after the employment appeals tribunal upheld its practice last April.
Mr Peace is believed to be considering further legal action and maintains police should have been called in early on to investigate the complaints against him.