Flying Fish is credited with having sunk a total of 58,306 tons of Japanese shipping and received 12 battle stars for World War II service.

During her voyage, a United States Army Air Forces plane mistook her for a Japanese submarine and dropped depth charges on her, but she submerged and avoided damage.

Continuing her first full war patrol, she searched major shipping lanes in the seas around Japan and scored a hit on a Japanese destroyer off Formosa during the night of 3 July 1942.

On 28 August, only three days after arriving on station, Flying Fish sighted the masts of a Japanese battleship (now known to be Yamato),[8] guarded by two destroyers and air cover.

Immediately the counterattack began, and as Flying Fish prepared to launch torpedoes at one of the destroyers, rapidly closing to starboard, her commanding officer was blinded by a geyser of water thrown up by a bomb.

When Flying Fish daringly came up to periscope depth 2 hours later, she found the two destroyers still searching, aided by two harbor submarine chasers and five aircraft.

Two hours later a second patrol craft came out, and as Flying Fish launched a stern shot, the Japanese ship opened fire, then swerved to avoid the torpedo.

Three times on this third patrol she launched bold attacks on Japanese task forces, only to suffer the frustration of poor torpedo performance, or to score hits causing damage which postwar evaluation could not confirm.

On 9 March 1943, three crewmen of the Flying Fish - Lyman Darol Williams,[9] Leonard Mathis Sturms,[10] and Harley Albert Kearney[11] died after drinking wood alcohol at the Royal Hawaiian Hotel in Waikiki during their rest and recreation in Honolulu, Hawaii.

On 12 April, she closed the northern coast to make a daring attack on the cargo vessel Sapporo Maru No.12 (2865 tons) which she sank, again in the presence of scout planes and armed trawlers.

Moving north to Hokkaidō, Flying Fish damaged a large freighter on 13 April, and two days later torpedoed the inter-island transport ship Seiryu Maru (1904 tons) which beached itself in a mass of flames.

Her first attacks, two against the same convoy, resulted in unconfirmed damage, but off Taiwan on 2 July, she blasted the stern off of the merchant passenger/troop transport Canton Maru (2822 tons) watching it sink.

While Pearl Harbor-bound from her patrol area, she made a two-day chase for a fast convoy, but was forced by her dwindling fuel supply to break off the hunt.

On 11 July she destroyed the 125-foot (38 m) sailing vessel Japanese guard boat Takatori Maru No.8 (51 tons) with gunfire, leaving it aflame from stem to stern.

After a major overhaul at Pearl Harbor from 27 July to 4 October 1943, Flying Fish sailed on her seventh war patrol, again with her original skipper , bound for the Palaus.

Bound for Majuro at the close of her patrol, on April Fool's Day 1944, the submarine torpedoed and sank the freighter Minami Maru (2398 tons – formally the Norwegian Solviken).

Clearing Majuro harbor 4 May, Flying Fish sailed for her tenth war patrol, coordinated with the assault on the Marianas scheduled to open the next month.

Along with other American submarines, she then headed to take up a patrol station between the Palaus and San Bernardino Strait, from which she could scout any movement by the enemy fleet out of its base at Tawi in the Sulus while the Marines were landed on Saipan.

On 15 June, the day of the invasion, Flying Fish spotted a Japanese carrier force emerging from San Bernardino Strait bound eastward.

On 1 August 1944, Flying Fish was escorted out to sea from Brisbane, Australia, to begin her eleventh war patrol, this one taking her to Davao Gulf, the coast of Celebes, and along the shipping lanes from the Philippines to Halmahera.

On 8 August, Flying Fish and Flounder arrived in the Admiralty Islands and moored alongside the submarine tender USS Euryale (AS-22) to take on fuel.