She was laid down on 15 May 1940 by the Bethlehem Steel Co. (Fore River), Quincy, Massachusetts; launched on 6 September 1941; sponsored by Mrs. Margarita Coll de Santori; and commissioned on 28 February 1942.

Enterprise was hit in the battle, and San Juan, which had damaged a gun mount off Guadalcanal, escorted the carrier to Pearl Harbor, arriving on 10 September 1942.

[3] On 5 October, the cruiser again headed for the South Pacific, stopping first at Funafuti in the Ellice Islands to deliver a deck load of 20 mm guns to the marines who had just landed there.

During the last dive-bombing attack on the formation, one bomb passed through San Juan's stern, flooding several compartments and damaging, though not disabling, her rudder.

At the end of June 1943, during the occupation of New Georgia, San Juan's carrier group patrolled the Coral Sea for 26 days to prevent enemy interference.

San Juan then joined the aircraft carrier Essex on a raid on Kwajalein in the Marshalls, fighting off persistent torpedo plane attacks on 4–5 December.

San Juan arrived in Leyte Gulf on 13 June for repairs and then joined Bennington, on 1 July for more strikes on the Japanese home islands.

[3] San Juan's embarked unit commander, Commodore Rodger W. Simpson, was assigned responsibility for freeing, caring for, and evacuating Allied prisoners of war in Japan.

On 29 August, the ship entered Tokyo Bay and landed parties which liberated prisoners at camps at Omori and Ofuna and the Shanagawa hospital.

Three days later, she sailed on "Magic Carpet" duty to Nouméa and Tutuila, returning to San Pedro, California, on 9 January 1946 with a full load of troops.

She was struck from the Navy list on 1 March 1959 and sold on 31 October 1961 to National Metal and Steel Corporation, Terminal Island, Los Angeles, California, for scrapping.