Although it has been speculated that Chitose as a seaplane carrier also carried Type A midget submarines, only her sister ship Chiyoda had that capability.

Operating her original complement of Kawanishi E7K (Allied reporting name "Alf") and Nakajima E8N (Allied reporting name "Dave") floatplanes, she supported Operation Z, the surprise unopposed landing of the Imperial Japanese Army′s 21st Army at Bias Bay on the coast of China 35 miles (56 km) northeast of Hong Kong, on 12 October 1938.

[1] In December 1939, Chitose, the seaplane tender Kinugasa Maru, and 24 Kawanishi H6K (Allied reporting name "Mavis") flying boats were stationed at Truk.

[1][3] The occasion was the first time that Chitose and many other new Japanese naval vessels — including the seaplane carriers Chiyoda and Mizuho and the heavy cruisers Tone and Chikuma, which had extensive floatplane-handling capabilities — were displayed to the public.

On 8 December, Chitose and Mizuho were attached to the 2nd Fleet to operate as part of the Fourth Surprise Attack Force, tasked with providing air cover for amphibious landings at Legaspi in southeastern Luzon in the Philippine Islands.

[4] From their anchorage, the two ships launched floatplanes to escort an invasion convoy heading for Manado in northern Celebes, make reconnaissance flights, and conduct a harassing bombing raid on an Allied radiotelephone station.

[1] In a friendly fire incident, one E13A from Mizuho shot down an Imperial Japanese Navy Yokosuka L3Y (Allied reporting name "Tina") carrying SNLF paratroopers when it flew low over the anchorage without responding to recognition signals.

[4] Chitose and Mizuho departed Bangka Island on 21 January 1942 and proceeded to the waters off Kendari on the southeastern coast of Celebes, patrolling the waters ahead of an invasion convoy carrying SNLF forces bound for Kendari, their aircraft conducting combat air and antisubmarine patrols over and around the convoy.

[1] On 26 January, Chitose separated from Mizuho, departing Sarabangka Bay bound for the Bangka Island anchorage accompanied by destroyers.

[1] She rendezvoused with Mizuho south of Mangole Island at 10:00 on 30 January 1942,[4] and the two seaplane carriers spent the day in the Manipa Strait, providing cover for Japanese invasion forces approaching Ambon and conducting harassing bombing raids against Namlea on Buru that doubled as reconnaissance flights.

[4] The weather subsequently improved, and on 1 and 2 February 1942 floatplanes from both ships provided air and antisubmarine defense to the Japanese invasion convoy, devoted about 70 sorties each day to heavy attacks against Allied ground forces on Ambon, and patrolled over the Banda Sea.

[4] They anchored off Cape Puting on 27 February 1942 and conducted air operations that day during the Battle of the Java Sea, although bad weather at the anchorage allowed them to launch few aircraft.

[4] On 28 February 1942 — the day of the Japanese landings on Java — Chitose and Mizuho anchored off the west coast of Bawean Island.

[4] They sighted no ABDA ships, but did observe three gunboats and eight torpedo boats in the channel at the main Dutch naval base at Sarabaya.

[4] At 09:45, they curtailed ground-support operations to focus on protecting the Japanese invasion fleet from air attack, and during the day E13A1s from the two ships claimed three Allied Northrop light bombers shot down, but much of what they did on 1 March is ambiguous or poorly documented.

[1] A strike by Chitose and Mizuho aircraft as well as floatplanes from the heavy cruisers Ashigara, Myōkō, Nachi, and Haguro sometime between 13:00 and 14:30 inflicted damage that caused flooding and disabled one of Pope′s propeller shafts.

[1] Later, a strike by six Nakajima B5N (Allied reporting name "Kate") torpedo bombers from the aircraft carrier Ryūjō attacked Pope, and Ashigara and Myōkō intercepted and sank her at 15:40.

[1][4] On 2 March 1942, Chitose and Mizuho set up a seaplane base at Karangdawa, 3 miles (4.8 km) east of Cape Awarawara, from which they continued to support the Java landings.

[4] After routine maintenance and repairs, they got underway from Staring Bay on 9 March 1942 to return to the combat area at Cape Awarawara, but Dutch forces on Java surrendered that day.

[1] As the convoy approached Midway on 3 June 1942, nine U.S. Army Air Forces B-17 Flying Fortresses bombed it and U.S. Navy PBY Catalina amphibious aircraft attacked it with torpedoes, but Chitose escaped damage.

[1] Chitose was detached from the Midway Invasion Force on 7 June 1942 and proceeded to Wake Island in company with the heavy cruisers Haguro and Myōkō and three destroyers.

[1] At 18:20, two SBD Dauntless dive bombers from Bombing Squadron 3 (VB-3) aboard Saratoga attacked Chitose, damaging her port engine and hull plates and set three F1M2s on her deck on fire.

[1] En route, seven B-17 Flying Fortresses of the U.S. Army Air Forces 11th Heavy Bombardment Group attacked the ships, but inflicted no damage on them.

[1] Based on the floatplane's sighting report, the aircraft carrier Zuikaku launched an airstrike against the convoy which sank the destroyer USS Meredith (DD-434).

[5] While Chitose was at sea off Tawi-Tawi conducting air training on 22 May 1944, the U.S. Navy submarine USS Puffer (SS-268) fired a spread of torpedoes at her at 09:24, but they exploded in her wake and she escaped damage.

On 15 June 1944, with U.S. forces landing on Saipan, Operation A-Go was activated, and Chitose headed for the Marianas along with the rest of the 1st Mobile Fleet.

[5] With the Marianas campaign underway, the activation of Operation A-Go resulted in the Japanese 1st Mobile Fleet meeting U.S. Navy Task Force 58 in the two-day Battle of the Philippine Sea on 19–20 June 1944.

Around dawn on 25 October, the Battle off Cape Engaño — one of several actions making up the Battle of Leyte Gulf — began when Ozawa launched a small airstrike against Task Force 38 which suffered heavy losses and accomplished nothing Task Force 38 counterattacked with a series of large, punishing airstrikes.

At 08:35, a line of three large explosions — either torpedo hits or near-misses by bombs — took place on Chitose′s port side forward of the Number 1 aircraft elevator.

[5] At 09:37, an hour after her initial wounds, in the Philippine Sea at position 19°20′N 126°20′E / 19.333°N 126.333°E / 19.333; 126.333, Chitose capsized to port and nosed under, with the loss of 904 men.