Following trials, S-36 operated along the United States West Coast until the summer of 1925, with interruptions for exercises in Alaskan waters in June 1923 and for fleet maneuvers in the Caribbean Sea during the winter of 1924.

She was then assigned to the United States Asiatic Fleet, departing the U.S. West Coast in mid-September 1925, and arriving at the Submarine Base, Cavite Navy Yard, Luzon, Philippines, on 4 November 1925.

For the next sixteen years, S-26 remained in the western Pacific, conducting exercises and patrols and undergoing overhauls at Cavite during the winter, and operating off the China coast from Tsingtao during the summer months.

With the increase of hostilities on the mainland, however, summer deployments were shortened and individual patrols were extended throughout the Philippines, into the South China Sea, and in 1938, into the Dutch East Indies.

Still unable to transmit and with worsening air and salt water leaks, S-36 proceeded to Mariveles, anchoring there four days later.

Repairs were made over the next few weeks and stores replenished, and she then started a final patrol in Philippine waters before heading south to join Allied forces gathering in the Dutch East Indies.

Clearing Mariveles Bay on 30 December 1941, she immediately commenced patrolling the Verde Island Passage between Luzon and Mindoro.

On 1 January 1942, she reconnoitered the north and east coast of Batangas Bay, then moved to the west and south of Verde Island.

In mid-afternoon, she sighted a small Japanese transport moored to the seawall at Calapan, Mindoro, fired one torpedo, and claimed the sinking of the target.

On 8 January, the port engine air compressor failed, and, because of battery water consumption and the distance and time involved in the transit to the Dutch East Indies, she began making her way south.

On the morning of 15 January, at the approximate intersection of the Sibutu-Makassar and Davao-Tarakan routes, diving was delayed by oil supply failures to the starboard engine, and she was spotted by a Japanese destroyer.

Still in critical condition of trim and propulsion, S-36 cleared the area and about noontime began making repairs to her port main motor.

Both port and starboard shafts went out of commission during the day and one man collapsed from the heat, but the main motor lube oil pumps were repaired.

For over twenty-four hours the crew battled to save the submarine, but chlorine gas generated by her flooded forward battery and the sea conditions combined against them.