On 25 August 1941, Kitakami returned to Sasebo for conversion to a "torpedo cruiser" with ten Type 92 quadruple torpedo tube mounts for the 61-cm long-range oxygen-propelled Type 93“Long Lance”torpedoes (a total of 40 tubes), in line with Imperial Japanese Navy plans to create a special “Night Battle Force” of torpedo-cruisers. Modification was complete by 30 September 1941, and Kitakami is assigned to the Japanese First Fleet, CruDiv 9, under Rear Admiral Fukuji Kishi.
From January to May 1942, Kitakami was assigned largely to training duties in Japanese home waters. At the time of the Battle of Midway on 29 May 1942, Kitakami and its sister ship Ōi were part of the Aleutian Screening Force, and return safely to Japan on 17 June 1942.
CruDiv 9 was disbanded on 21 November 1942, and the Kitakami was assigned directly to the Combined Fleet. In November, the Kitakami transported troops from Manila to Rabaul, New Britain, and returned to Sasebo by the end of the year.
In January 1943, Kitakami was assigned to the reinforcement of Japanese forces in New Guinea, and escorted a convoy with the IJA 20th Infantry Division from Pusan to Wewak, New Guinea via Palau. In February, Kitakami escorted a convoy with the IJA 41st Infantry Division from Tsingtao to Wewak, again via Palau.
On 15 March 1943, Kitakami was re-assigned to CruDiv 16 of the Southwest Area Fleet under Admiral Takasu, as a guard ship based out of Surabaya. It escorted three troop convoys from Surabaya to Kaimana, New Guinea during April and May.
On 23 June 1943, while at Makassar, the Kitakami, Ōi, Kinu and Kuma were bombed by Consolidated B-24 Liberators of the 5th Air Force's 319th Bomb Squadron. None of the cruisers were hit, but some sustained slight damage from near-misses.
After refit at Seletar Naval Base, Singapore in August, Kitakami escorted a troop convoy from Singapore to the Nicobar Islands in early September. Two more convoys were escorted to Port Blair, Andaman Islands in late October.
In late January 1944, Kitakami escorted another convoy to Port Blair. On its return voyage while transiting Malacca Strait, southwest of Penang, Malaya, on 27 January 1944, the Kitakami was hit aft by two torpedoes fired by the HMS Templar (P316). The Kinu took Kitakami in tow to Angsa Bay, Malaya for emergency repairs, followed by extensive repairs at the No. 101 Repair Facility at Seletar Naval Base, Singapore in February. Repairs were not completed until 21 June 1944. However, after departing Singapore to escort the tanker Kyokuto maru, Kitakami began to take on water and had to put into Cavite Navy Yard in the Philippines from 12 July 1944 to 26 July 1944. Despite the additional repairs, Kitakami still took on water on its return voyage to Sasebo.
On 19 March 1945, American Task Force 58 aircraft carriers USS Essex (CV-9), USS Intrepid (CV-11), USS Hornet (CV-12), USS Wasp (CV-18), USS Hancock (CV-19), USS Bennington (CV-20) and the USS Belleau Wood (CVL-24) made the first carrier attack of the war on Kure Arsenal. More than 240 aircraft (SB2C Helldivers, F4U Corsairs and F6F Hellcats) attacked the battleships Hyuga, Ise, Yamato, Haruna, aircraft carriers Amagi, Katsuragi, Ryuho, Kaiyo and other ships. Kitakami sustained no damage.
In July 1945, an additional twenty seven single mount Type 96 25-mm AA guns were fitted to Kitakami. However, on 24 July 1945 about 200 aircraft Task Force 38's USS Essex (CV-9), USS Ticonderoga (CV-14), USS Randolph (CV-15), USS Hancock (CV-19), USS Monterey (CVL-26) and USS Bataan (CVL-29) again attacked the Kure area. Kitakami was damaged by strafing and thirty-two crewmen were killed.
Capt. Teiji Sakamoto - 15 April 1921 - 15 March 1922
Capt. Masashi Yamazaki - 15 March 1922 - 1 December 1922
Capt. Ritsuto Takahashi - 1 December 1922 - 1 December 1923
Capt. Togo Kawano - 1 December 1923 - 1 November 1924
Capt. Makoto Yoshikawa - 1 November 1924 - 4 December 1928
Cmdr. / Capt. Shosuke Shimomura - 4 December 1928 - 5 October 1929 (Promoted to Captain on 10 December 1928.)
Capt. Naohiko Saito - 5 October 1929 - 5 December 1929
Capt. Baron Minoru Sonoda - 5 December 1929 - 1 December 1930
Capt. Rokuro Horie - 1 December 1930 - 14 November 1931
Capt. Jinichi Kusaka - 14 November 1931 - 1 December 1932
Capt. Baron Tomoshige Samejima - 1 December 1932 - 14 March 1934
Capt. Moriji Takeda - 14 March 1934 - 15 November 1934
Capt. Yasuo Inoue - 15 November 1934 - 10 October 1935
Capt. Mitsuharu Matsuyama - 10 October 1935 - 1 December 1937
Capt. Hajime Horiuchi - 1 December 1937 - 15 December 1938
Capt. Masao Ueno - 15 December 1938 - 19 October 1940
Capt. Shigeyasu Nishioka - 19 October 1940 - 1 November 1940
Capt. Shunsaku Nabeshima - 1 November 1940 - 1 September 1941
Capt. Tsutau Araki - 1 September 1941 - 28 November 1941
Capt. Saiji Norimitsu - 28 November 1941 - 5 September 1942
Capt. Nobumichi Tsuruoka - 5 September 1942 - 17 May 1943
Capt. Tomekichi Nomura - 17 May 1943 - 2 November 1943
Capt. Jo Tanaka - 2 November 1943 - 10 June 1944
Capt. Saburo Kase - 10 June 1944 - 29 August 1944
Capt. Masamoto Shimizu - 29 August 1944 - 1 December 1944
Capt. Kunizo Kanaoka - 1 December 1944 - 15 August 1945