Nagara, as with the other vessels of her class, was intended for use as the flagship of a destroyer flotilla, and it was in that role that she participated in the invasions of the Philippines and the Dutch East Indies after the attack on Pearl Harbor.

The Nagara-class vessels were essentially identical to the earlier Kuma-class cruisers, using the same hull design, powerplant and layout of armament.

[3] Soon after commissioning, Nagara was assigned to the Japanese naval base at Port Arthur, from where she patrolled the China coast to Qingdao.

As the Second Sino-Japanese War continued to escalate, Nagara was assigned to provide cover for Japanese transports during the Battle of Shanghai,[4] and remained on station patrolling the China coast and the Yangtze River through 1939.

With the heavy cruisers Myōkō and Nachi, Nagara participated in the Hainan Island Operation in February 1939 under Vice Admiral Nobutake Kondō.

[4] Returning to the Celebes on 4 February 1942, Rear Admiral Kubō transferred his flag back to Nagara, which then covered the invasion of Makassar.

In the middle of the night of 6 February 1942, the invasion force was sighted by the submarine USS Sculpin, which mistook Nagara for a Tenryū-class cruiser and fired two Mark 14 torpedoes; one missed and the other prematurely exploded.

[4] On 17 February 1942, Nagara provided escort for transports with the Imperial Japanese Army's 48th Infantry Division for the invasion of Bali and Java.

After Akagi was hit and set afire by dive bombers from USS Enterprise, Vice-Admiral Nagumo transferred his flag to Nowaki and then to Nagara.

The fleet included the aircraft carriers Shōkaku, Zuikaku, Ryūjō, battleships Hiei and Kirishima, cruisers Tone and Chikuma, and destroyers Akigumo, Makigumo, Kazagumo, Yūgumo, Akizuki, Hatsukaze, Nowaki, Amatsukaze, Maikaze, Tanikaze and Tokitsukaze.

[4] On 9 November 1942, Rear Admiral Kimura and the Nagara squadron was assigned to screen Hiei and Kirishima during a reinforcement plan to land 14,500 men, heavy weapons and supplies on Guadalcanal.

Most notably, Hiei had been struck by two 8-inch (203 mm) shells from the heavy cruiser USS San Francisco which jammed her rudder in a hard turn, unable to maneuver.

In early February, Nagara participated in the evacuation of Guadalcanal, recovering 11,700 surviving Imperial Japanese Army troops.

Nagara was relieved as flagship of 2nd Destroyer Flotilla by the newly commissioned cruiser Noshiro on 20 August 1943, and was reassigned to the IJN 8th Fleet under Vice Admiral, Baron Tomoshige Samejima.

On 14 November 1943, she assisted in towing the light cruiser Agano back to Truk after it had been torpedoed by the submarine USS Skate.

It was attacked by Grumman TBF Avenger torpedo-bombers and Douglas SBD Dauntless dive bombers from Task Group 50.3's aircraft carriers USS Enterprise and Essex and damaged enough to justify a return to Japan in January 1944.

She remained in Japanese home waters training with new destroyers and escorting a convoy to the Ogasawara Islands in June and to Okinawa in July.

[4] On 7 August 1944, en route from Kagoshima to Sasebo, Nagara was spotted by the submarine USS Croaker on her first war patrol.