Arriving at Manila on 5 November, she joined the Asiatic Fleet and, through the winter of 1925, engaged in exercises with surface and submarine units in Philippine waters.

For the next fifteen years, S-41’s schedule, and that of her division, remained basically the same; summer months were spent in Chinese waters, winters in the Philippines.

That year was spent at Cavite and Olongapo for overhauls; in the South China Sea for fleet exercises; and in the waters off Luzon on patrol.

After hearing of Japan's attack on Pearl Harbor, she patrolled off Looc Bay, Tablas Island, in an attempt to impede the Japanese offensive.

Thirteen days later, she torpedoed a Japanese transport off Cape Mangkalihat and was credited with a kill by the American-British-Dutch-Australian Command (ABDA).

She fired on several enemy ships, including a submarine with probable damage, and her patrol was noted for its "absence of serious material failures" — an achievement unique in boats of her class at that time.

Moving to the Guadalcanal area later in the patrol, S-41 was operating 5 nautical miles (9.3 km; 5.8 mi) from Savo Island when a ship moving at high speed — which her commanding officer identified as a possible cruiser — passed her in the predawn darkness of 24 August 1942 after she submerged and three depth charges exploded close enough to her to shatter light bulbs.

Her crew then discovered that S-41 had missed an earlier message ordering her to a new station, leading her commanding officer to wonder if S-41 had been the subject of friendly fire attacks by Allied ships who had not expected a U.S. submarine at S-41′s location on 24–25 August 1942.

On 27 May, she scored a probable kill on a four-masted fishing schooner; and, in the pre-dawn darkness of 31 May, she torpedoed a cargo ship in a night surface attack.

Her name was struck from the Naval Vessel Register on 25 February 1946; and, in November of that year, her hulk was sold, for scrapping, to the National Metal and Steel Corporation, Terminal Island, Los Angeles, California.