Singer was born in New York City. He was adopted and grew up in a Jewish household in New Jersey. He attended West Windsor-Plainsboro High School South (formerly just West Windsor-Plainsboro High School), then studied filmmaking at New York's School of Visual Arts and later USC School of Cinema-Television in Los Angeles. Actors Lori and Marc Singer are his cousins. He is Jewish and openly gay, and has said that his life experiences of growing up as a minority influenced his development of the X-Men movies.

His production company, Bad Hat Harry Productions, produces House and works in television, film, and video game media. It is named after a line from Jaws, one of his favorite films. The line, "That's some bad hat, Harry", is heard over the company's end credit animation.

He is a producer on the Fox show House.