An employment tribunal said EduAction, which won a contract in 2001 to manage education in the London borough of Waltham Forest, would have treated Valarie Lestrade differently if she had been white.
Afro-Caribbean Ms Lestrade, a successful head who led Church Mead junior school out of special measures, claimed she was abused by an office manager and received "hostile comments" from white members of staff to new racial awareness training.
The tribunal said EduAction failed to investigate her complaints properly and discriminated against her by suspending her, suggesting she was to blame for deteriorating relationships at Church Mead.
Now the company and Waltham Forest Council face a huge compensation bill after being found guilty of racial discrimination.
Ms Lestrade, 53, told The TES this week: "I am appalled at the way I've been treated." EduAction has appealed against the decision and refused to comment.
Ms Lestrade joined the school in November 1999, and her headship was praised by Ofsted. However, the tribunal heard she "experienced difficulties" with an office manager, who was suspended but reinstated following an investigation by officials from EduAction.
Ms Lestrade made other complaints of racism. The tribunal heard that the reaction to new race awareness training, in 2002, was "not overwhelmingly supportive" and was met with comments such as: "We (white people) have rights in this country."
She left temporarily in March 2003 to have surgery but her return was blocked by EduAction who said her replacement - a white senior teacher - was better placed to lead the school through a forthcoming Ofsted inspection.
While on leave, EduAction sent Ms Lestrade a letter criticising her leadership, including high staff turnover and poor book-keeping, even though "none of the matters" had been raised before.
When she eventually returned in January 2004, she was subjected to a leaflet campaign calling for her to go. EduAction failed to investigate this.
Ms Lestrade was eventually suspended in October 2004, pending an investigation into further claims that she misspent the budget and failed to tackle complaints by teachers.
The suspension was lifted in August 2005 but she was subsequently made redundant when the school closed and reopened under a new name.