Target availability and effectiveness of anti submarine efforts had major impact on use of deck guns for both KM and USN submarines. As decisions were made by KM to remove deck guns from U-boats, decisions were being made in USN submarine force to standardize deck gun with a 5" 25Cal wet gun (up from 3" 50Cal and 4" 50Cal) and the 40MM wet gun. In early 1945 several fleet boats were armed with two 5" 25Cal deck guns and two 40 MM guns, and given a rudimentary gun fire control system. the 40 MM while designed as an Anti Aircraft Gun was used on USN submarines only against surface vessels. The decision to develop submarine "gunboats" was driven by the fact that almost all Japanese warships and merchant ships were sunk and submarines were now targeting coasters, junks, and sampans which were not worth a torpedo. One boat, USS Blenny SS-324 on one of her last patrols during the war sank 63 such vessels with deck guns and boarding parties using demolition charges. There was also a famous "gun fight" in late October 1944 between heavily damaged USS Salmon SS-182 and two Japanese escort vessels. Unable to dive and with nothing to loose, Salmon charged the closest Japanese escort. She took all the fight out of the escort with several 4" shell hits (sighting down the bore of the gun) and then while passing alongside bow to stern at 50 yards range, the 20MM gunner on the forward sponson shot the entire drum of shells (60 rounds of HE, Incindiary, and tracer) into the bridge while two machine gunners on Salmon's bridge shot several belts of .50Cal sweeping the main deck of the escort. Salmon left the escort astern and smoking, then exchanged long range gun fire with the second escort before escaping into a rain squall.

The last USN submarine with deck guns was USS Perch APSS-313. She carried a 40MM on the cigarette deck and another 40MM on the sponson forward of the bridge. Perch used them in combat in Viet Nam as late as 1964 to provide covering fire for a SEAL team that came under attack during the extraction at the end of their mission.