[2] It is named after San Francisco, California, supervisor Harvey Milk, the first openly gay man to be elected to a public office in the United States.

The small program of a little over a dozen students was originally located in the Washington Square United Methodist Church and was run in collaboration with the New York City Board of Education.

[3] HMHS was created as an alternative education program for youth who find it difficult or impossible to attend their home schools due to threats, violence, or harassment.

[citation needed] HMHS came to national attention in 2002, when the Board of Education authorized a $3.2 million capital expansion of the school as one of its last acts prior to becoming a mayoral agency.

Independent mayor Michael Bloomberg supported the renovation of the school while Democratic N.Y. State Senator Rubén Díaz opposed it.