In mid-May 1939, she conducted tests with experimental periscopes, then prepared for her shakedown cruise which, between 26 June and 26 August, took her from Newfoundland to Venezuela and the Panama Canal Zone and back to southern New England.

From March to October 1941, she operated out of both Pearl Harbor and San Diego, California, then departed the former for her new base, Cavite, Philippines.

Clearing Manila Bay, Saury moved north to search for and intercept ships of the Japanese invasion force.

Then, on 21 December, she was ordered into Lingayen Gulf in response to a report from submarine Stingray (SS-186) of Japanese forces there.

Prior to dawn on 22 December, she took up patrol duties off San Fernando in the northern approaches to the gulf, and moved south.

After dark, she moved back into the gulf, past the enemy patrol line between San Fernando and Cape Bolinao.

That evening brought a change in orders; and, in preparing to clear the area, Saury found herself between two enemy ships.

On 19 January, the Japanese landed at Sandakan in North Borneo, and Saury arrived at Balikpapan to fuel and provision.

On 30 January, she met a Dutch patrol vessel off Meinderts Reef, then proceeded through Madura Strait to Surabaya (Soerabaja).

On 9 February, as the Japanese were taking Makassar, Saury departed Surabaya for her second war patrol.

On 24 February, she shifted northward to an area southeast of Sepandjang Island where she sighted and attacked, unsuccessfully, an enemy convoy.

From 26 February to 8 March, Saury patrolled from Meinderts Reef to Kangean Island, the eastern entrance to Madura Strait.

On 28 April 1942, Saury cleared Fremantle for her third war patrol, but, three days later, a crack in the after trim tank caused her to return to Australia.

She remained in the area for two days to intercept enemy traffic to Kendari; then moved north to hunt in Greyhound Strait and the Molucca Passage.

On 8 June, the submarine turned south and began retracing her route through the Molucca Passage and Greyhound Strait.

On 15 June, she searched Boeton Passage; then moved into the Flores Sea, whence she headed via Timor for Australia.

The next day, she sighted and attempted to close a tanker; then shifted her patrol to a line five miles (8 km) off the coast.

Saury returned to Pearl Harbor on 16 April 1943 and, on 7 May, she departed for her sixth war patrol which would take her into the East China Sea to operate off the northern Ryukyu Islands and in the coastal waters of Kyūshū.

During the patrol, she would also test the effectiveness of the high periscope in daytime attacks and the usefulness of the bathythermograph in locating thermal layers in which to hide.

On 25 May, the submarine entered her assigned area and headed toward Amami Ōshima, a naval base some 200 miles (300 km) south of the industrial port of Kagoshima on southern Kyūshū.

On the afternoon of 28 May, Saury, patrolling on the surface with her high periscope in operation, sighted the masts of a steamer and moved to intercept.

In the late afternoon of 29 May, Saury, again on the surface and using the high periscope, sighted smoke about fourteen miles (21 km) off.

Poor weather then slowed her westward progress still further; and, on the night of 30 July, while halfway between Iwo Jima and Okinawa, she made her first contact of the patrol.

During repair and refit, Saury was given an enlarged conning tower, new periscope shears, and new radar equipment.

On her eighth and ninth war patrols, 4 October to 26 November 1943 and from 21 December 1943 to 14 February 1944, Saury inflicted no damage.

Much of the latter patrol was spent in fighting extremely bad weather in the East China Sea, during which proper navigational positions were unobtainable.

The wave overtook Saury from the quarter, pushed her over to a 40-degree list to port; turned her 140 degrees from her course; and sent green water through the conning tower hatch and main induction.

However, the glassy sea, unlimited visibility, and enemy, land-based, patrol planes combined against her, and she broke off the attack.

She patrolled in the Nansei Shoto area from 20 September to 4 November, rescuing a downed pilot, but sinking no enemy ships as she hunted in the wake of the fast carrier forces.

After stopping at Saipan from 5 to 10 November, she proceeded on the second phase of the patrol, an antipatrol vessel sweep north of the Bonin Islands.