On her first war patrol - 24 May-16 July - Pipefish cruised west of the Mariana Islands, as a rescue submarine for pre-invasion carrier strikes on Saipan, saving one pilot on 12 June.

On her third war patrol - 28 October 1944 – 6 January 1945, Pipefish roamed southwest of Taiwan and off the east coast of Hainan Island, China, operating with Pampanito, Sea Cat, and Searaven.

On her fourth war patrol - 31 January to 26 March - Pipefish provided rescue capability for downed aviators in the Nansei Shoto area.

During her fifth war patrol - 28 April to 16 June - she performed lifeguard duty for B-29 Superfortress aviators off Honshū, and in the Nanpō Islands area.

Her sixth war patrol - 15 July-28 August - called for lifeguard duty in the Nanpō Islands area and off the east coast of Kyūshū.