An employment tribunal has found that Gad's Hill school near Rochester, in Kent, had unfairly dismissed Lorna Hurrell, aged 54, and discriminated against her on grounds of disability.
The tribunal said she had been forced to leave last summer because the school feared she might become ill again, even though the medical prognosis was encouraging.
Mrs Hurrell was head of the kindergarten department of the pound;5,000-a-year, co-educational school, which has 270 pupils aged three to 16.
She was initially diagnosed with cancer in early 2000 and returned to work after treatment.
Later the tumour was found to have spread and she needed further treatment.
Again, this was successful and she was declared fit to work in April 2002.
But her specialist recommended a phased return and said she should not resume full duties until the autumn.
But the school insisted she either return full-time straightaway or take a severance package. When she refused both options, she was told her contract would be terminated.
Mrs Hurrell took her case to the tribunal with the support of the National Union of Teachers. Dick Boland, the union's regional secretary, said: "I applaud her courage."
Members in independent schools were entitled to the same legal protection and union support as those in the state sector, he stressed.
A tribunal in June will determine the level of compensation.