Due to its protracted development, a shortage of experienced pilots and the United States Navy's achievement of air superiority by the time of its introduction, the B6N was never able to fully demonstrate its combat potential.

The B5N carrier-based torpedo bomber's weaknesses had shown themselves early in the Second Sino-Japanese War; as well as updating that aircraft, the Imperial Japanese Navy began seeking a faster, longer-ranged replacement.

In December 1939 it issued a specification to Nakajima for a Navy Experimental 14-Shi Carrier Attack Aircraft capable of carrying the same external weapons load as the B5N.

In order to lessen increased wingloading due to the heavier powerplant, Fowler flaps were installed which could be extended beyond the wing's trailing edge.

[3] The B6N1's Mamoru 11 engine was found prone to severe vibrations and overheating at certain speeds and was at first judged too unreliable, an important consideration given that the plane was expected to fly long distances over open water.

Some attempts were also made to use RATOG (rocket-assisted take-off gear) units on several B6N1s in order to qualify the aircraft for use on smaller carriers but the results were unsatisfactory.

As the Mamoru 11 and Kasei 25 were similar in size, installation was relatively straightforward, requiring only that the nose be extended to maintain the aircraft's center of gravity and minor alterations to the oil cooler and air intakes on the engine cowling.

A smaller 3.4 m (11 ft) diameter four-bladed propeller and shorter spinner were also installed at this time, resulting in a small weight-savings, and the retractable tailwheel was fixed permanently in the down position.

Finally, the single exhaust stacks on either side of the engine cowling were replaced with multiple smaller stubs to reduce glare at night and to supply a minor amount of forward thrust.

The intent was to gradually replace all of the B5N Kate torpedo bombers then operating aboard the carriers of the Third Fleet at Truk Atoll in the Caroline Islands.

[10] On 19 June 1944, the B6N made its carrier-borne combat debut at The Battle of the Philippine Sea, operating in an environment where the U.S. Navy had virtually complete air superiority.

[11] [12][13] B6N2 c/n 5350 remains in existence and it is stored at the National Air and Space Museum's Paul E. Garber Preservation, Restoration, and Storage Facility in Suitland, Maryland.