Elaine Hunter, National Union of Teachers official at the International school, Birmingham, lost her job after clashing with Sir Dexter Hutt.
Flashpoints included public criticism of the head's discipline policies, which centre on sending badly-behaved pupils to an isolation unit, a row over proposed redundancies and complaints of too much pressure on staff.
Mrs Hunter also balloted NUT members on whether the union should mount a campaign pushing for the International school to leave the Ninestiles federation - a group of schools run by Sir Dexter.
She was suspended on May 25 last year and local press reports said she was "led out of a packed classroom" by a senior member of staff and the school's bursar.
This week, a panel of governors upheld the school's earlier decision, made in November, to sack Mrs Hunter on the grounds of gross misconduct.
Mrs Hunter, a psychology and sociology teacher, who is pursuing legal action against the school for unfair dismissal, told The TES: "They have not sacked me for my teaching. I've been dismissed for trying to represent my fellow teachers. I think this sets a very dangerous precedent."
Mrs Hunter, a former civil servant, joined the International in 1999, four years before it became part of the Ninestiles federation of schools under Sir Dexter's executive headship.
Birmingham council confirmed Mrs Hunter had been dismissed but said no further comment would be made.
Her dismissal this week came as it emerged that Sir Dexter, who is said to be one of Tony Blair's favourite headteachers and was knighted in 2004 for services to education, is about to relinquish leadership of the International school.
The council said that the partnership had "run its natural course" and key targets, including improved GCSE results and attendance and a fall in fixed-term exclusions, had been met.
Ruth Robinson, the headteacher who managed the day-to-day running of the International, will also leave at the end of the school year.
In the last three years the Department for Education and Skills and the council have paid more than pound;1 million to Ninestiles Plus - Sir Dexter's education consultancy company, run from his own school, Ninestiles, in the Acocks Green area of Birmingham - to manage the International school.
Another inner-city comprehensive, Waverley, left the federation last year, although in January this year Ninestiles Plus won another contract to run the Central Technology College in Gloucestershire.