Mooney's mother, Lala, was a Cuban refugee who escaped from political imprisonment at the age of 21, shortly after the Bay of Pigs Invasion. He's related to his mother's older brother, former Miami mayor Xavier Suarez and his son, current mayor Francis X. Suarez. From a family of Irish immigrants, his father Vincent grew up in Long Island, New York. Mooney was born in 1971 in Washington D.C. and raised in Frederick, Maryland. He graduated from Frederick High School, where he was elected as president of the student government.