After shakedown at New London, Connecticut, Gato departed 16 February 1942 via the Panama Canal for San Francisco, California, where she underwent additional training.

On her first war patrol from Pearl Harbor (20 April – 10 June 1942), Gato unsuccessfully attacked a converted aircraft carrier 3 May before being driven away by the fierce depth charging of four destroyers off the Marshall Islands.

She obtained four torpedo hits with unconfirmed damage to a ship 15 August 1942, and terminated her patrol at Dutch Harbor, Alaska.

Gato was overhauled at Mare Island; returned to Pearl Harbor 22 August 1943; and conducted her sixth war patrol (6 September – 28 October) via Truk and Bougainville in the Solomons to Brisbane.

En route on 19 October she attacked a convoy, scoring hits for unknown damage to two large cargo ships.

She rescued a Japanese soldier from a life raft on 16 December, then attacked a convoy in the Saipan-Massau traffic lanes four days later to sink cargo ship Tsuneshima Maru and scored damaging hits on another freighter.

After two hours of dodging depth charges, she finally evaded her attackers, surfaced, and headed for Tingmon, the most likely port for the damaged cargo ship.

Gato discovered a live depth charge on her deck at the same time two enemy escorts were sighted headed in her direction.

On the night of 22 – 23 April she had a brief contest with two Japanese submarines and narrowly missed destruction as well-aimed torpedoes came close.

Between 27 and 30 April she rescued 10 Army aviators from shallow water near the beaches of Cape Toi Misaki, Kyūshū.

A Gato-class submarine was used for a portion of the stock footage in the 1959 motion picture Up Periscope starring James Garner and Edmond O'Brien.