Flounder arrived at Milne Bay, New Guinea, from New London, Connecticut, on 6 March 1944, and 11 days later sailed on her first war patrol, bound for the Palau Islands.

In the Philippine Sea during the assault on the Mariana Islands, Flounder made a sound contact on 17 June which resulted in her sinking the 2,681-ton transport Nipponkai Maru.

On 24 June, as Flounder sailed on the surface, two enemy planes suddenly dived out of the cloud cover, and dropped bombs which landed close aboard, causing some minor damage.

Flounder took on provisions and fuel at Mios Woendi, New Guinea, from 28 August to 1 September, then completed her patrol in Davao Gulf, returning to Brisbane on 4 October.

[7][8] An attack by Flounder's group on a convoy off Palawan on 21 November 1944 sank the freighter Gyosan Maru (5,698 tons), but other contacts were few, and the sub returned to Fremantle to refit between 13 December and 7 January 1945.

Underway for her fifth war patrol, Flounder had to return to Fremantle from 12 to 14 January to repair her fathometer, then sailed to lead a three-submarine coordinated attack group in the South China Sea.

Returning to Pearl Harbor action-bound on the day hostilities ended, Flounder was ordered to the East Coast, and arrived at New York City on 18 September.