After a month's training in Lake Michigan, Hammerhead was placed in a floating drydock and towed down the Mississippi River to New Orleans, Louisiana, where she arrived on 8 April 1944.

She departed Fremantle 9 September and made her first attack the night of 1 October, when a convoy consisting of four cargo ships, one oiler, and three escorts was detected off Borneo.

[7] The morning of 20 October the submarine found still another six ship convoy, and after evading one of the escorts delivered a six-torpedo attack.

The submarine returned from this highly successful patrol 2 November 1944, and was later awarded the Navy Unit Commendation for her outstanding performance.

Due to the illness of her commanding officer, the submarine was forced to end her patrol, and moored at Subic Bay 3 March 1945.

After missing with two torpedoes at extreme range the submarine found the mark in a second attack, sinking the tanker Kinrei Maru.

Sighting a cargo carrier 14 May with only an aircraft escort, Hammerhead made a perfect approach and sank the ship with two torpedoes.

Hammerhead departed Fremantle 21 June on her seventh and last war patrol, also carried out in the Gulf of Siam, in company with three other submarines.

Earmarked for loan under the Military Assistance Program, Hammerhead was converted to a GUPPY submarine at Mare Island Naval Shipyard and recommissioned once more 16 July 1954 to prepare for transfer.