Apogon was laid down on 9 December 1942, by the Portsmouth Navy Yard in Kittery, Maine; launched on 10 March 1943; sponsored by Mrs. Helen Lorena Withers (née LaBar), wife of Admiral Thomas Withers, Jr., then Commander of Submarine Forces; and commissioned on 16 July 1943.

[citation needed] The submarine held shakedown in the waters off the New England coast and departed New London on 13 September, bound for Hawaii.

Apogon transited the Panama Canal on 25 September and reported for duty on that date to the Commander in Chief, Pacific Fleet.

Her patrol area comprised the waters within a 60-mile (110 km) radius of Moen Island and those along the shipping lanes between Truk and Kwajalein.

After a brief stop at Johnston Island on 5 November to top off her fuel tanks, Apogon continued on to her assigned area.

However, when a crewman was preparing to clean a 20 millimeter machine gun the next day, a live cartridge accidentally left in the chamber discharged and ricocheted into the man's leg.

Apogon began her fourth patrol, which was in the area between Formosa and the Philippines, in company with Guardfish, Thresher, and Piranha.

On 12 July, Apogon and her wolf pack consorts spotted a nine-ship Japanese convoy sailing with approximately six escorts.

The leading Japanese ship of the center column of the formation apparently sighted the wake of Apogon's periscope and turned back to ram the submarine.

As Apogon was turning to port to bring her stern tubes to bear, she was struck on the starboard side by the freighter.

She arrived at Midway on 22 July, where crews installed additional bracing on the periscope shears before the submarine proceeded on to Pearl Harbor.

After a month of refit, Apogon commenced her sixth patrol on 20 November, again sailing for the Kuril Islands.

[citation needed] Apogon received six battle stars for her World War II service.