Bushra Nasir, head of all-girls Plashet school, in Newham, east London, was named professional of the year at a ceremony in London.
She said: "I feel very proud and very privileged, particularly as I was the only educationist in the category. I think this is brilliant for education, for state schools and for Muslim women."
Mrs Nasir, 52, who is married and has three children became the first Muslim secondary head when she took up her post in 1993. Since then she has turned around the school with 72 per cent of pupils now achieving five or more top grade GCSEs.
She is chair of the GTC's resources and planning committee, and president of the Muslim Teachers' Association.
Mrs Nasir was awarded a CBE in the Queen's Birthday Honours in 2003, and in 2000 received the Windrush Award for being an educational high-flier.
Stephen Irwin QC, one of the judges, said: "Bushra is outstanding. She has completely turned the school around and is an ideal role model for the staff and children.
"She exemplifies how you can balance the role of a professional headmistress with the demands of local political and social issues."
Mrs Nasir was presented with a glass plaque by Cherie Blair, and introduced to the Prince of Wales and the Duchess of Cornwall.
Sashi Sivaloganathan, vice-chairman of the GTC, was shortlisted in the awards in the public sector category.
The women were the only representatives from the education world nominated for the awards.