In October 1939, Perch departed San Diego, California, for Manila where she became a division flagship and made a summer cruise in 1940 to Tsingtao and Shanghai.

A week before Japan's attack on Pearl Harbor, Perch rendezvoused with two transports off Shanghai and escorted the 4th Marine Regiment from China to the Philippines.

Failing to detect any, she shifted to an area off Hong Kong, and on the evening of 25 December 1941 launched four torpedoes at a large merchant ship, all missing.

In a night attack on a large merchant ship off the eastern coast of Celebes, Perch was hit in the superstructure, forward of the pressure hull of the conning tower, by a high-explosive round which blew away the bridge deck, punctured the antenna trunk and temporarily put her radio out of commission.

Hoping to score a kill before the reverse happened, Perch climbed to around 90 feet deep, but it was too late, Minegumo and Natsugumo were right on top of her and furiously unleashed their depth charges.

Minegumo and Natsugumo assumed their target had perished and continued on, but Perch had enough integrity to remain under water, surfacing after 2 hours in the early morning of the 2nd and began sailing for repairs.

Perch lied motionless underwater, and when sunrise broke, Ushio and Sazanami launched a final depth charge attack which caused the most critical damage of all before leaving the area, concluding they had sunk their target.

An attempt to dive was made, but it almost sank the ship then and there, and meaning the crew found out the hard way Perch was completely incapable of underwater travel and resurfaced for the last time.

The blinkering light emitted by the cigar was spotted by Captain Tameichi Hara aboard the Japanese destroyer Amatsukaze, which quickly trained her guns on the submarine and fired away.

The next morning, Captain Hara called Amatsukaze's crew to the deck to graduate them on their kill, and decided to ban smoking on the ship due to the experience.

Lieutenant Kenneth G. Schacht was awarded a Navy Cross for assisting in the scuttling of Perch and therefore preventing the Japanese from capturing classified code books, materials, and equipment.