The second Perch (SS–313) was laid down 5 January 1943 by the Electric Boat Co., Groton, Conn.; launched 12 September 1943; sponsored by Mrs. David A. Hart; and commissioned 7 January 1944, Lt. Comdr. Blish C. Hills in command.
On 29 April she departed Pearl Harbor with for Midway where joined them. The South China Sea was the hunting ground for the wolf pack. Early in the morning of 24 May, a medium tanker was contacted and damaged by four torpedo hits. The counterattack by a lone escort prevented further observation of the damage inflicted and knocked out both high pressure air compressors by flooding of the pump room. Perch headed for the Marshall Islands, arriving Majuro 4 June.
Perch departed Pearl Harbor on her third war patrol 19 September. At Midway she joined submarines and and the three set out for the confined waters of the East China and Yellow Seas. Perch unsuccessfully attacked one heavily escorted transport, and performed lifeguard duty supporting B-29 raids on Honshū. Perch then headed for Saipan to refuel en route to Brisbane, Australia, for duty with Submarines, Southwest Pacific Fleet.
The fourth war patrol began 19 December from Brisbane. First Perch patrolled off Hainan, China; next off Singapore; and finally in Balabac Straits off Borneo. She sighted no enemy ships, and the patrol ended at Fremantle, Western Australia, 15 February 1945.
On 12 March Perch departed Fremantle carrying with her eleven Australian specialists trained in commando warfare. On the first night of the mission, in the Makassar Straits, above Balikpapan, Borneo, she landed four of the party who were to make a reconnaissance of the beach and surrounding territory. Coming in close ashore two nights later to disembark the remainder of the party, Perch contacted a 300-ton coastal freighter that threatened to cut off her return to open water. Perch engaged with gunfire and with the second hit the freighter burst into towering flames and sank. Perch returned to Fremantle, Western Australia, completing her fifth war patrol.
On 15 April Perch departed Fremantle on her sixth war patrol and journeyed to the Java Sea to hunt out the enemy. When she contacted a convoy of two ships, an alert Japanese escort discovered Perch and subjected her to a severe two-hour depth charging which caused considerable damage throughout the boat. She then sailed to the China coast to patrol off Hainan before returning to Pearl Harbor 5 June.
On 11 July Perch departed Pearl Harbor and after fueling at Saipan, proceeded north for duty in the "Lifeguard League" off Japan. On 13 August she rescued a Navy Corsair pilot from the water two miles offshore, bombarded fishing vessels and buildings on the beach, and retired to sea. A few hours later the same day, she picked up another pilot from the same fighter squadron five miles offshore. Two days later Japan capitulated and Perch returned to Pearl Harbor 30 August.
Perch departed Pearl Harbor and set course for the Golden Gate, arriving Hunter's Point 8 September. She decommissioned and was placed in reserve in January 1947. On 19 January 1948 Perch was redesignated as a Submarine Transport, SSP–313, and was placed in an active status, attached to the U.S. Pacific Fleet.
Perch recommissioned at Mare Island Naval Shipyard 20 May 1948, Lt. Comdr. O. H. Payne in command. Through 1949, the ship participated in various troop- and cargo-carrying exercises. On 31 January 1950 Perch was reclassified a Transport Submarine, ASSP-313. In September 1950 Perch transported a force of British Commandos in a raid on the northeast coast of Korea west of Tanchon. The target, a train tunnel on the north-south supply line, was destroyed, with the loss of one man who was buried at sea. The commanding officer, Lt. Comdr. R. D. Quinn, became the only submarine commanding officer to receive a combat award during the Korean conflict when he was awarded the Bronze Star for this action.
From August 1951 to March 1952, Perch underwent overhaul at Mare Island. From 1952 to 1954, Perch trained, making "reconnaissance-runs" and "raids" on several Alaskan and Hawaiian islands. In January 1955 Perch made a cruise to WestPac conducting a "reconnaissance and raid" on Iwo Jima and observed other islands in the Bonin Chain. Periods between Far Eastern cruises, Perch performed type training and intertype amphibious exercises in the San Diego area.
Perch, again classified as a Submarine Transport, APSS-313, on 24 October 1956, departed San Diego 5 November for a reconnaissance exercise in the Panama Canal Area, returning to San Diego 11 December. In late 1957 she made a reconnaissance voyage from San Diego to Hawaii and Alaska, and spent most of 1958 and 1959 in amphibious training exercises in the San Diego area with marines and Underwater Demolition Teams.
Perch recommissioned 11 November 1961, Lt. Comdr. C.H. Hedgepeth in command, trained on the West Coast and Hawaii through 1962, and arrived at her new homeport, Subic Bay, Philippine Islands in March 1963. Her operations consisted of training the U.S. Marine's Amphibious Recon Battalion, Army Special Forces, and Navy UDTs in reconnaissance and also in providing training services to allied countries. In May and June 1964 Perch traveled to Mindoro and trained with British commando forces. July and August were spent in Hong Kong, Pohong Bay, Korea (with R.O.K. Special Forces), Yokosuka and Okinawa, Japan.
March and April 1965, saw Perch participating in exercise "Jungle Drum III" by landing 75 Marine Corps reconnaissance personnel on the Malay Peninsula from the Gulf of Siam. Perch conducted search and rescue operations in the Vietnam combat zone during August and September. She made two amphibious landings on the coast of South Vietnam during November and December as part of operation "Dagger Thrust."
During January Perch landed UDT personnel for beach survey work in South Vietnam as part of operation "Double Eagle." She then provided services at Legaspi, P.I. to train Filipino and American UDT personnel. Between local training operations in the Subic Bay area, Perch worked with Chinese Special Forces at Kaohsiung, Taiwan, and with Army Special Forces at Keelung, Taiwan.
In July Perch participated in operation "Deck House II" on the coast of South Vietnam. Again in August, Perch conducted several independent beach surveys with UDT personnel along the coast of South Vietnam. For operation "Deck House IV" in September Perch landed UDT personnel on five successive nights for preinvasion beach reconnaissance. On 7 October 1966, Perch headed for Pearl Harbor via Hong Kong, Palau Islands, Guam, and Midway Island. She operated in Hawaiian waters until 1967 when she became Naval Reserve Training submarine at San Diego. On 22 August 1968 Perchs classification was changed from APSS–313 to Submarine Transport LPSS–313'.
Perch was designated an Unclassified Miscellaneous Submarine IXSS-313 30 June 1971 She was decommissioned and struck from the Naval Register, 1 December 1971, and Disposition, sold for scrapping, 15 January 1973.