Mr Perry, 44, visited Quintin Kynaston comprehensive in north London last term - although he was not in drag. The male artist, whose alter-ego, "Claire", dresses in childlike party frocks, interviewed eight Year 12 and 13 boys about their attitudes to transvestism.
The interviews formed part of Men in Frocks, a Channel 4 documentary screened this week, in which Mr Perry explores British views on cross-dressing.
Gary Kynaston, deputy head, said: "In a multi-cultural, multi-ethnic school, situations occur which challenge students on a daily basis. Schools need to challenge pupils in as many ways as possible, forcing them to justify their opinions."
He believes that broadening pupils' perspectives should be a central part of citizenship: "Inviting in a transvestite fits in with the type of citizenship activities schools normally do. We involve police, magistrates, MPs. It's important for students to know that a diverse range of viewpoints exists in the modern world."
Mr Perry, who started cross-dressing at the age of 12, agreed it was vital to address prejudice among children. "The absolute enemy of trannies is a gaggle of 14-year-old school girls," he said. "In a group, they will have no inhibitions about saying what they think: 'You're disgusting, you're insulting to women.' They're so conservative at that age.
"There are still basic misconceptions about trannies, that they're gay or freaks. There probably are gays and freaks among transsexuals, but no more than in any other section of the population."
Mr Perry was not allowed to meet the boys in drag, and interviewed them dressed as a man. "Grayson Perry is an individual who happens to be a transvestite," Mr Kynaston added. "You can't do things just for shock value. You need to discuss transvestism in depth, as part of a broader discussion of sex and sexuality."
But a spokeswoman for the Institute for Citizenship questioned whether inviting transvestites into school was a productive use of lesson time.
She said: "The critical issue is for young people to be active political, social and moral citizens, engaged with civic institutions. These more mainstream issues should be the focus, even if they don't have that frisson of sexual excitement."