At the time of the attack on Pearl Harbor, Naka was engaged in the invasion of the southern Philippines as part of Vice Admiral Ibo Takahashi's Third Fleet escorting transports with components of the IJA 48th Infantry Division.

In January 1942, 4th Destroyer Flotilla was assigned to the invasion of the Netherlands East Indies, escorting a convoy carrying the Kure No.

[2] On 24 January 1942 while landing troops at Balikpapan, the Royal Netherlands Navy submarine HNLMS K XVIII, operating on the surface due to poor weather, fired four torpedoes at Naka, but missed.

In late February 1942, 4th Destroyer Flotilla escorted transports with the 48th Infantry Division to Makassar, Celebes and eastern Java.

[4] At 1603, Naka and its destroyer squadron with Asagumo, Minegumo, Murasame, Harukaze, Samidare and Yūdachi launched 43 Type 93 Long Lance torpedoes at the Allied force from about 16,250 yards (14,860 m); sinking Kortenaer.

[5] Landing operations progressed without opposition on 31 March 1942, however, the submarine USS Seawolf fired four torpedoes at Naka, but all missed.

The convoy was intercepted by the submarine USS Shad in the East China Sea on 23 October 1943, which fired 10 torpedoes, failing to damage either cruiser.

On 3 November 1943, convoy was attacked 60 nautical miles (111 km) north of Kavieng by 13th Air Force Consolidated B-24 Liberator bombers.