The aircraft was deployed in 1942, referred to as the "Suisen 2" ("Hydro fighter type 2"), and was only utilized in defensive actions in the Aleutians and Solomon Islands operations. Such seaplanes were effective in harassing American PT boats at night, and they were very difficult to detect, even with primitive radar. Close misses killed officers and crews of boats such as PT 105. They could also drop flares to illuminate the PTs which were vulnerable to destroyer gunfire, and depended on cover of darkness. Since the boats left a phosphorescent wake which was visible from the air, they would leave their engines in idle to minimize this. It was primarily for this reason that John F. Kennedy's PT 109 was caught off guard in idle and rammed by the destroyer Amagiri, unable to maneuver out of the way in time.

The seaplane also served as an interceptor for protecting fueling depots in Balikpapan and Avon Bases (Dutch East Indies) and reinforced the Shumushu base (North Kuriles) in the same period. Such fighters served aboard seaplane carriers Kamikawa Maru in the Solomons and Kuriles areas and aboard Japanese raiders Hokoku Maru and Aikoku Maru in Indian Ocean raids. In the Aleutian Campaign this fighter engaged with Lockheed P-38 Lightning fighters and Boeing B-17 Flying Fortress bombers. The aircraft was used for interceptor, fighter-bomber, and short reconnaissance support for amphibious landings, among other uses.

Later in the conflict the Otsu Air Group utilized the A6M2-N as an interceptor alongside Kawanishi N1K1 Kyofu ("Rex") aircraft based in Biwa lake in the Honshū area.

 The last A6M2-N in military service was a single example recovered by the French forces in Indochina after the end of World War II. It crashed shortly after being overhauled.

The large float and wing pontoons of the A6M2-N degraded its performance by about 20%, enough that the A6M2-N was not usually a match for even the first generation of Allied fighters. All A6M2-Ns were built by Nakajima.