Assigned to Submarine Division 17 on commissioning, S-40 operated off Southern California until January 1924, when she proceeded to Panama, thence continued into the Caribbean Sea.

Engaging in Fleet Problems II, III, and IV en route to and during her stay there, she returned to San Diego, California, in late March.

During the winter of 1925, she conducted exercises in sound and target approaches, crash dives, and torpedo firing in the waters off Luzon.

During the summer of 1940, however, hostilities on the Asiatic mainland brought a change in her schedule and she conducted increasingly extended "familiarization" cruises among the Philippine Islands and in adjacent waters.

Early on 23 December, S-40 sighted the enemy; fired four torpedoes, unsuccessfully, at a transport, then, for much of the remainder of the day, remained submerged, avoiding depth charges dropped by the Japanese screening forces.

After dark, she anchored in Agno Bay; made temporary repairs to her hull, engines, pumping system, and port air compressor; then patrolled off Bolinao.

On 30 December, three days before Manila and Cavite fell, S-40 departed Luzon and pointed her bow toward the Netherlands East Indies.

She arrived at Soerabaja on the north coast of Java on 2 February, her crew frustrated by their attempts to intercept enemy shipping, but with information on tides, currents, navigational aids, and Japanese tactics.

Initially assigned to intercept enemy traffic into the Salamaua-Lae area of New Guinea, she was ordered to the Solomon Islands on 2 July to relieve S-38, which had been forced to vacate her position off Tulagi.

S-40 patrolled between Tulagi and Lunga Roads and off Savo Island; fired on a maru, but did not score; then shifted to the New Georgia-Santa Isabel area to intercept Rabaul shipping.

Thence, she crossed the Solomon Sea to the D'Entrecasteaux Islands off Papua to impede the movement of enemy reinforcements into Milne Bay.

Repairs to S-40’s deteriorating main motor cables and attempts to correct fuel leaks into the after battery occupied the next three weeks.

Further training exercises were carried out prior to reaching Attu, where she topped off and departed again on 30 June, heading for the Kuril Islands.

S-40’s ninth war patrol, from 12 August to 10 September, was again conducted in the fog and heavy swells of the northern Kurile Islands, but was cut short by repeated material failures which included the seemingly ever present problems of deterioration of the main power cables and fuel oil leaks into the after battery.