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Rear Admiral John H. Maurer entered the Naval Academy at Annapolis in 1931. Upon his graduation in 1935 with the degree of Bachelor of Science, he reported to the battleship USS Colorado as a junior officer. In 1939 he attended the Submarine School, New London, Connecticut, after which he was assigned to the USS Pickerel. In February 1941 he was transferred to the USS Tarpon, where he was serving as Engineer and Navigator at the outbreak of World War II. While on the Tarpon he participated in the defense of Corregidor, and was detached as Executive Officer in June 1942. 

He next served on the USS Harder as Executive Officer from pre-commissioning through her third war patrol in the Pacific, during which time the Harder won the Presidential Unit Citation. RADM Maurer then assumed command of the USS Atule at her commissioning in June 1944 and participated in operations at Leyte, Iwo Jima, Okinawa Gunto, and in the Third Fleet operations against Japan. RADM Maurer also took part in the "Nanook" Arctic Cruise of the Atule in 1946, before he decommissioned that submarine in the fall of 1947. 

He then reported to the Office of Naval Research, Washington, D.C., where he served as Head of the Weapons Branch, Naval Science Division and later as Director of the Scientific Information Division. From July 1948 until May 1950 he was Assistant to the Director of the Plans and Operations Division, Armed Forces Special Weapons Project at Sandia Base, Albuquerque, New Mexico. For a year thereafter, he served on the Staff of Commander, Submarine Squadron One as Gunnery and Torpedo Officer. For three months he served as Acting Commander, Submarine Division 11. While so assigned, he also served as Officer in Charge of the Prospective Commanding Officers School, and on the Staff of Commander, Submarine Force, Pacific. 

From July 1951 to July 1952 he had command of Submarine Division 11, with additional duty as Commander, Submarine Element, Western Pacific, Naval Forces Far East during Korean hostilities. He returned to the Navy Department in Washington in 1952 and for two years served as Assistant to the Director of Nuclear Energy Applications, Research and Development Division, Bureau of Ordnance. RADM Maurer was a student at the National War College, Washington, D.C., from August 1954 to June 1955, after which he commanded Submarine Squadron Seven until August 1956. He then reported as Assistant Chief of Staff for Operations and Plans and later served as Chief of Staff to Commander Submarine Force, Pacific. 

From October 1958 until October 1959 he served as Commanding Officer of the USS Hassayampa (AO-145), and subsequently as Commanding Officer of the USS Saint Paul (CA-73), the flagship of Commander Seventh Fleet in the Western Pacific, homeported in Yokosuka, Japan. In 1960 he reported as Chief of Staff and Aide to Commander, Submarine Force, Atlantic. In March 1962, he assumed duties as the Director of Submarine Warfare in OPNAV, the Pentagon. In November 1963 RADM Maurer became Director of Naval Warfare Analyses in the Office of the Chief of Naval Operations. In July 1964, he was assigned as Commander Middle East Force, his last assignment prior to this. RADM Maurer assumed the duties of Commander Submarine Force, U.S. Pacific Fleet on June 11, 1966.