Captain John Joseph Cowan CSC, CD (born 23 July 1957) is a Royal Australian Navy (RAN) officer.
Cowan originally joined the Royal Canadian Navy (RCN) in 1976 as an ordinary seaman boatswain, eventually being commissioned as an officer in 1988, but transferred to the RAN in 1996.
He was the commissioning Commanding Officer of HMAS Choules (2011–12).