John Mooney may refer to:

John Mooney is an American basketball player from Altamonte Springs, Florida who plays as a small forward for the Notre Dame Fighting Irish basketball team.

John Mooney (born August 6, 1964) is an American sprint canoer who competed from the mid-1990s to the early 2000s (decade). He won a gold medal in the K-2 200 m event at the 1995 ICF Canoe Sprint World Championships in Duisburg.

John Mooney (born September 4, 1966) is a former vice-president of the Transport Workers Union (TWU) Local 100, the union of New York City Transit Authority employees in New York City.

John Patrick Mooney (January 22, 1933 – March 29, 2003) was a Canadian politician. He served in the Legislative Assembly of New Brunswick as a Liberal member from the constituency of Saint John South.