When first deployed, the AJ-1 was too large and heavy to be used by any American aircraft carrier except for the Midway class. The modernized Essex class carriers with reinforced decks and the very large Forrestal class could also handle the Savage. The aircraft was not popular aboard ship as "it was so big and cumbersome that it complicated any other flight operations the ship was required to conduct." One problem was that the wings had to be folded one at a time by a crewman on top of the fuselage with a portable hydraulic pump, a time-consuming process, so that the bomber could be moved out of the way to allow other aircraft to land or take off. One pilot reported that the AJ-1 was "a dream to fly and handled like a fighter", when everything was working properly. The aircraft, however, was not very reliable, possibly because it was rushed into production before all the bugs could be worked out.
Early in the Savage's career, squadrons would typically deploy a detachment to Naval Air Station Port Lyautey, Morocco, for service with the Sixth Fleet and fly the bombers aboard as needed. The plan was that the Savages would then be loaded with atomic bombs already aboard the carriers and launched once the carriers were in the Eastern Mediterranean Sea. The tactic to deliver the bombs was to fly at low level through Bulgaria and Romania before climbing at maximum power to the proper altitude to release the bomb. The aircraft would then perform a wingover maneuver and dive to low altitude, keeping the tail of the aircraft aimed at the target to avoid serious damage from the shock wave of the explosion.
VC-5 made the first of its three deployments to Port Lyautey in February 1951. VC-6 (Composite Squadron 6) received its first Savages in late 1950 and deployed to Port Lyautey in October 1951 before transferring to the Pacific Fleet in October 1952. In July 1953 it deployed a detachment of two aircraft to K-3 Air Base in Korea to act as a nuclear deterrent. VC-7, VC-8, and VC-9 received their AJ-1s beginning in June 1951 and all remained on the East Coast of the United States. The Navy redesignated all of its Savage-equipped composite squadrons as heavy attack squadrons (VAH) on 1 November 1955. The squadrons retained their existing numbers except for VC-8 which became VAH-11 as all East Coast squadrons were odd-numbered.
AJ tankers were used to refuel John Glenn's Vought F8U-1P Crusader during the Project Bullet transcontinental speed record flight in July 1957; AJ-2s from VAH-6 on the West Coast and AJ-1s from VAH-11 on the East Coast. Beginning in 1957 the Douglas A3D Skywarrior began to replace the Savages in the VAH Squadrons. Their refueling role was continued by the formation in January 1958 of VAH-15 on East Coast and VAH-16 on the West Coast. Both squadrons were equipped with AJ-2s, but both were short-lived and disbanded early the following year.
The AJ-2P was flown by VJ-61 (Photographic Squadron) and VJ-62, both of which were redesignated VAP-61 (Heavy Photographic Squadron) and VAP-62, respectively, on 2 July 1956. VJ-61 was assigned to the Pacific Fleet and VJ-62 to the Atlantic Fleet. The squadrons never deployed as complete units, but rather deployed as one to three aircraft detachments. Detachment Queen was formed by VJ-61 during the Korean War at Naval Station Sangley Point, in the Philippines, to fly reconnaissance missions over the People's Republic of China and North Korea. The detachment continued its missions after the war until at least June 1954. Both squadrons frequently provided photographic mapping for agencies outside the Navy like the Army Map Service, the Army Corps of Engineers, the U.S. Coast and Geodetic Survey and the U.S. Departments of the Interior and Agriculture. The AJ-2s in these squadrons were replaced by Douglas A3D-2P Skywarriors beginning in 1959, although the last month that they were reported in squadron service was January 1960. Surviving AJ-1 and AJ-2 aircraft became A-2As and A-2Bs, respectively, when the Department of Defense redesignated all U.S. military aircraft in a common series in 1962.
Three AJ-2s were loaned to the National Aeronautics and Space Administration as weightlessness simulators from January 1960 to September 1964. They were eventually destroyed during firefighting training. Three AJ-1s were purchased by AJ Air Tankers, Inc. in early 1960 for use as water bombers. Their turbojets were removed before the delivery flight to California, during which one aircraft crashed. The two surviving aircraft were fully modified for the role after delivery and could carry 2,000 US gallons (7,600 l; 1,700 imp gal) of fire retardant. They first flew missions during the 1961 fire season. Another aircraft crashed on takeoff in September 1967 when an engine failed and the sole survivor only made a few more flights before it was scrapped in 1968–69.
At least one other AJ-2 was purchased and used as a water bomber before it was purchased in 1970 by Avco Lycoming for use as an engine testbed for the YF102 turbofan. The J33 turbojet had to be reinstalled and the aircraft required almost a year of maintenance before it could be flown to Avco Lycoming's home airfield at Stratford, Connecticut. The YF102, too fat to fully fit in the bomb bay, was mounted on a retractable mechanism that could be lowered below the aircraft for tests. The testing was conducted from January to July 1972. Another round of testing on the commercial derivative of the F102, the ALF 502, was performed between January 1979 and December 1980. In 1984, routine maintenance discovered several loose rivets on the spar and further examination showed that the skin was starting to separate from the spar. This damage was too uneconomical to repair so Avco Lycoming decided to donate the last surviving Savage to the National Museum of Naval Aviation. The AJ-2 was flown to Naval Air Station Pensacola in Pensacola, Florida on 9 May 1984.