Mooney was born in San Diego, California to parents Brian Mooney and Linda Kozub. He graduated from Scripps Ranch High School in 2003 where he won Best Actor as Prospero in Shakespeare's The Tempest. Mooney attended the University of Southern California and majored in Film. He performed improv and sketch comedy with collegiate group Commedus Interruptus. In 2003 the three new members added to Commedus were Kyle Mooney, Beck Bennett, and Nick Rutherford. In 2007 the same three would form the sketch comedy group "Good Neighbor" along with Kyle's best friend, director and editor Dave McCary. Bennett and McCary are joining Mooney on SNL.