S-36's keel was laid down on 10 December 1918, just weeks after the Armistice ended World War I, at the Bethlehem Shipbuilding Corporation yard in San Francisco. She was launched on 3 June 1919 and commissioned on 4 April 1923. After trials and operations along the West Coast, she was assigned to the United States Asiatic Fleet in 1925, arriving at the submarine base at Cavite Navy Yard in the Philippines that November. For the next sixteen years, S-36 lived the rhythm of the Asiatic Fleet: overhauls at Cavite in winter, patrols off the China coast from Tsingtao in summer, with the patrol range expanding into the South China Sea and, by 1938, the Dutch East Indies as tensions in the Pacific escalated.

On 2 December 1941, S-36's scheduled overhaul was cancelled. She was ordered north on patrol, loading water, stores, and torpedoes before departing Cavite at one in the morning on 3 December. She reached Bolinao harbor and waited. On 8 December, word came: the Japanese had attacked. Hours later, she sighted enemy aircraft and began patrol duties. Then the failures started. Air leaks on the 9th. On the 10th, her crew listened helplessly to radio traffic as Japanese bombers destroyed Cavite, the base they had left just days before. Their radio operator could not raise the station afterward. Electrical steering failed on the 12th. Exhaust valve leaks on the 13th. By the 14th, none of her outgoing messages had gotten through. She limped to Mariveles at the entrance to Manila Bay, anchoring there four days later for repairs.

Patched together, S-36 cleared Mariveles Bay on 30 December and began working south toward the Dutch East Indies. On New Year's Day 1942, she fired a torpedo at a Japanese transport at Calapan, Mindoro, claiming a sinking that Japanese records never confirmed. Then the machinery began failing in earnest. The port engine air compressor gave out on the 8th. The starboard compressor followed on the 10th. The port main motor died on the 13th. On the morning of 15 January, delayed by oil supply failures while trying to dive, she was spotted by a Japanese destroyer. With one engine out, S-36 submerged and prepared to fire, but the destroyer was faster. Seven depth charges detonated around the boat, knocking out bow plane controls, blowing fuses, and sending her gyrocompass spinning. Her main motor bearing began to smoke, requiring a crewman to hand-oil it continuously with a squirt gun. At 230 feet, she lost depth control and began rising. Life jackets were issued. At 90 feet, the crew arrested the ascent. By 0705, the destroyer had given up the hunt.

S-36 continued south through Makassar Strait, her machinery failing and reigniting in an exhausting cycle. Fire broke out in the main motor circulating pump on the 16th. Both shafts went out of commission on the 17th. A crewman collapsed from the heat. At 0404 on 20 January, the end came suddenly: S-36 ran hard aground on Taka Bakang Reef, approximately 60 nautical miles west-northwest of Makassar, Celebes. For over 24 hours, her crew fought to save the boat, but chlorine gas from the flooded forward battery and worsening sea conditions worked against them. A plain-language distress call brought the Dutch launch Attla, which evacuated most of the crew. Lieutenant John R. McKnight Jr. and the remaining hands stayed aboard for one last attempt. When the Dutch cargo ship Siberote arrived, McKnight accepted the inevitable, transferred his men, and scuttled S-36 by flooding at 1330 on 21 January. Every crewmember survived. The boat did not.