On 3 October, Snapper was assigned to Submarine Squadron (SubRon) 3 based at Balboa, Canal Zone, where she participated in training and fleet exercises until 15 March 1939, when she set sail for repairs at the Portsmouth Navy Yard.

Departing Portsmouth on 9 May, she stopped at New London, Connecticut, and then got underway for the West Coast, arriving at San Diego, California, on 2 June.

On 1 July, the submarine set sail for Pearl Harbor and maneuvers in the Hawaiian area, followed by overhaul at the Mare Island Navy Yard in Vallejo, California, from 1 December 1939 to 1 March 1940.

Except for a brief voyage to San Diego in October and November 1940, Snapper remained in the Hawaiian area participating in training exercises and fleet tactics until 3 May 1941, when she departed for overhaul at the Mare Island Navy Yard.

On 19 December, Snapper departed Manila for her first war patrol, covering the shipping lanes between Hong Kong and Hainan Strait until 8 January 1942, when she set sail for Davao Gulf in the Philippines.

On 1 February, as the submarine approached Bangka Strait, she was detected by an enemy destroyer which made a fruitless depth charge attack.

Arriving there on 4 April, she transferred her cargo to submarine rescue vessel Pigeon, took on board 27 evacuees, and headed back to Fremantle, evading Japanese destroyer patrols on the way.

On 28 September 1942, a PBY-5 Catalina flying boat of U.S. Navy Patrol Squadron 101 (VP-101) mistook her for a Japanese submarine and attacked her in the Indian Ocean 330 nautical miles (611 km; 380 mi) south-southwest of Bali at a position given by Snapper as 12°59′S 113°42′E / 12.983°S 113.700°E / -12.983; 113.700 and by the PBY-5 as 12°50′S 114°28′E / 12.833°S 114.467°E / -12.833; 114.467.

Snapper spent her tenth war patrol engaged in lifeguard duties near Truk in support of bombardment missions by the United States Army Air Forces.

As Snapper quickly dove, one bomb struck directly above the hatch instantly killing one crewman[6] and injuring several others, including the commanding officer.

Two wounded enlisted men were transferred to submarine tender Bushnell at Majuro Atoll on 13 June, and Snapper continued her lifeguard duty until returning to Pearl Harbor on 21 July.

On 5 September, Snapper departed Pearl Harbor for her eleventh and final war patrol, conducted in the Bonin Islands area.

Snapper was struck from the Naval Vessel Register on 30 April 1948 and sold for scrap to the Interstate Metals Corporation of New York City, on 18 May 1948.