After completing its shakedown cruise out of New London, Gabilan sailed for brief antisubmarine training at Key West before transiting the Panama Canal for the Hawaiian Islands.

Her second war patrol (29 June – 18 August) took her to the south coast of Honshū, Japan, where, on the night of 17 July, she made a daring radar chase through bright moonlight and phosphorescent water.

Her third war patrol (26 September – 12 November) took her south of the Japanese Empire in company with Besugo and Ronquil to detect the departure from Bungo Suido of any major enemy fleet units that might interfere with the liberation of the Philippine Islands.

The latter part of the patrol was spent in an independent search of approaches of Kii Suido where, in a dawn periscope attack on 31 October, she destroyed oceanographic research vessel Kaiyō No.

She joined Perch and Barbel in a coordinated patrol off the southern entrance to Palawan Passage and the western approach to Balapac Strait, where Japanese battleships Ise and Hyūga were expected to appear en route to threaten American invasion forces in the Philippines.

Gabilan outwitted three escorts to sink a small freighter the morning of 14 April 1945, then scored hits on two cargo ships of another convoy.

[7] Gabilan had difficulty diving in the heavy seas and broached, and the destroyers' gunfire straddled her an estimated ten times before she finally submerged undamaged to a depth of 150 feet (46 m).

Proceeding by way of San Francisco, California, and the Panama Canal Zone, Gabilan arrived at New London, Connecticut, where she decommissioned 23 February 1946 and joined the Atlantic Reserve Fleet.