Admiral Isoroku Yamamoto issued the code phrase "Niitaka yama nobore" (Climb Mount Niitaka) on 2 December 1941 from Nagato at anchor at Hashirajima to signal the 1st Air Fleet (Kido Butai) in the North Pacific to proceed with its attack on Pearl Harbor.
When the war started for Japan on 8 December, she sortied for the Bonin Islands, along with Mutsu, the battleships Hyūga, Yamashiro, Fusō, Ise of Battleship Division 2, and the light carrier Hōshō as distant cover for the withdrawal of the fleet attacking Pearl Harbor, and returned six days later.
Yamamoto transferred his flag to the new battleship Yamato on 12 February 1942.
Nagato was briefly refitted 15 March – 9 April at Kure Naval Arsenal.

In June 1942 Nagato, commanded by Captain Hideo Yano, was assigned to the Main Body of the 1st Fleet during the Battle of Midway, together with Yamato, Mutsu, Hosho, the light cruiser Sendai, nine destroyers and four auxiliary ships.
Following the loss of all four carriers of the 1st Air Fleet on 4 June, Yamamoto attempted to lure the American forces west to within range of the Japanese air groups at Wake Island, and into a night engagement with his surface forces, but the American forces withdrew and Nagato saw no action.
After rendezvousing with the remnants of the 1st Air Fleet on 6 June, survivors from the aircraft carrier Kaga were transferred to Nagato.
On 14 July, the ship was transferred to Battleship Division 2 and she became the flagship of the 1st Fleet.
Yano was promoted to Rear Admiral on 1 November and he was replaced by Captain Yonejiro Hisamune nine days later.
Nagato remained in Japanese waters training until August 1943.
On 2 August Captain Mikio Hayakawa assumed command of the ship.

That month, Nagato, Yamato, Fusō and the escort carrier Taiyō, escorted by two heavy cruisers and five destroyers transferred to Truk in the Caroline Islands.
In response to the carrier raid on Tarawa on 18 September, Nagato and much of the fleet sortied for Eniwetok to search for the American forces before they returned to Truk on 23 September, having failed to locate them.
The Japanese had intercepted some American radio traffic that suggested an attack on Wake Island, and on 17 October, Nagato and the bulk of the 1st Fleet sailed for Eniwetok to be in a position to intercept any such attack.
The fleet arrived on 19 October, departed four days later, and arrived back at Truk on 26 October.
Hayakawa was promoted to Rear Admiral on 1 November and he was relieved on 25 December by Captain Yuji Kobe.

On 1 February 1944, Nagato departed Truk with Fusō to avoid an American air raid, and arrived at Palau on 4 February.
They left on 16 February to escape another air raid.
The ships arrived on 21 February at Lingga Island, near Singapore, and the ship became the flagship of Vice Admiral Matome Ugaki, commander of Battleship Division 1, on 25 February until he transferred his flag to Yamato on 5 May. Aside from a brief refit at Singapore, the ship remained at Lingga training until 11 May when she was transferred to Tawitawi on 12 May. The division was now assigned to the 1st Mobile Fleet, under the command of Vice Admiral Jisaburō Ozawa.

On 10 June, Battleship Division 1 departed Tawitawi for Batjan in preparation for Operation Kon, a planned counterattack against the American invasion of Biak.
Three days later, when Admiral Soemu Toyoda, commander-in-chief of the Combined Fleet, was notified of American attacks on Saipan, Operation Kon was canceled and Ugaki's force was diverted to the Mariana Islands.
The battleships rendezvoused with Ozawa's main force on 16 June.
During the Battle of the Philippine Sea, Nagato escorted the aircraft carriers Jun'yō, Hiyō and the light carrier Ryūhō.
She fired 41 cm Type 3 Sankaidan  incendiary anti-aircraft shrapnel shells at aircraft from the light carrier Belleau Wood that were attacking Jun'yō and claimed to have shot down two Grumman TBF Avenger torpedo bombers.
The ship was strafed by American aircraft during the battle, but was not damaged and suffered no casualties.
During the battle Nagato rescued
Admiral Isoroku Yamamoto issued the code phrase "Niitaka yama nobore" (Climb Mount Niitaka) on 2 December 1941 from Nagato at anchor at Hashirajima to signal the 1st Air Fleet (Kido Butai) in the North Pacific to proceed with its attack on Pearl Harbor. When the war started for Japan on 8 December, she sortied for the Bonin Islands, along with Mutsu, the battleships Hyūga, Yamashiro, Fusō, Ise of Battleship Division 2, and the light carrier Hōshō as distant cover for the withdrawal of the fleet attacking Pearl Harbor, and returned six days later. Yamamoto transferred his flag to the new battleship Yamato on 12 February 1942. Nagato was briefly refitted 15 March – 9 April at Kure Naval Arsenal.
In June 1942 Nagato, commanded by Captain Hideo Yano, was assigned to the Main Body of the 1st Fleet during the Battle of Midway, together with Yamato, Mutsu, Hosho, the light cruiser Sendai, nine destroyers and four auxiliary ships. Following the loss of all four carriers of the 1st Air Fleet on 4 June, Yamamoto attempted to lure the American forces west to within range of the Japanese air groups at Wake Island, and into a night engagement with his surface forces, but the American forces withdrew and Nagato saw no action. After rendezvousing with the remnants of the 1st Air Fleet on 6 June, survivors from the aircraft carrier Kaga were transferred to Nagato. On 14 July, the ship was transferred to Battleship Division 2 and she became the flagship of the 1st Fleet. Yano was promoted to Rear Admiral on 1 November and he was replaced by Captain Yonejiro Hisamune nine days later. Nagato remained in Japanese waters training until August 1943. On 2 August Captain Mikio Hayakawa assumed command of the ship.
That month, Nagato, Yamato, Fusō and the escort carrier Taiyō, escorted by two heavy cruisers and five destroyers transferred to Truk in the Caroline Islands. In response to the carrier raid on Tarawa on 18 September, Nagato and much of the fleet sortied for Eniwetok to search for the American forces before they returned to Truk on 23 September, having failed to locate them. The Japanese had intercepted some American radio traffic that suggested an attack on Wake Island, and on 17 October, Nagato and the bulk of the 1st Fleet sailed for Eniwetok to be in a position to intercept any such attack. The fleet arrived on 19 October, departed four days later, and arrived back at Truk on 26 October. Hayakawa was promoted to Rear Admiral on 1 November and he was relieved on 25 December by Captain Yuji Kobe.
On 1 February 1944, Nagato departed Truk with Fusō to avoid an American air raid, and arrived at Palau on 4 February. They left on 16 February to escape another air raid. The ships arrived on 21 February at Lingga Island, near Singapore, and the ship became the flagship of Vice Admiral Matome Ugaki, commander of Battleship Division 1, on 25 February until he transferred his flag to Yamato on 5 May. Aside from a brief refit at Singapore, the ship remained at Lingga training until 11 May when she was transferred to Tawitawi on 12 May. The division was now assigned to the 1st Mobile Fleet, under the command of Vice Admiral Jisaburō Ozawa.
On 10 June, Battleship Division 1 departed Tawitawi for Batjan in preparation for Operation Kon, a planned counterattack against the American invasion of Biak. Three days later, when Admiral Soemu Toyoda, commander-in-chief of the Combined Fleet, was notified of American attacks on Saipan, Operation Kon was canceled and Ugaki's force was diverted to the Mariana Islands. The battleships rendezvoused with Ozawa's main force on 16 June. During the Battle of the Philippine Sea, Nagato escorted the aircraft carriers Jun'yō, Hiyō and the light carrier Ryūhō. She fired 41 cm Type 3 Sankaidan  incendiary anti-aircraft shrapnel shells at aircraft from the light carrier Belleau Wood that were attacking Jun'yō and claimed to have shot down two Grumman TBF Avenger torpedo bombers. The ship was strafed by American aircraft during the battle, but was not damaged and suffered no casualties. During the battle Nagato rescued 
Japanese battleship Nagato