His classmates included Michitaro Totsuka, Takeo Kurita, Rokuzō Sugiyama, Gunichi Mikawa and Aritomo Gotō.

After serving on the cruiser Kasuga and battleship Asahi, Kobayashi was sent to the United Kingdom as part of the crew bringing the new battlecruiser Kongō to Japan.

On graduation and promotion to lieutenant, Kobayashi served as chief navigator on the survey vessel Katsuriki and the aging cruiser Akitsushima.

With the start of the Second Sino-Japanese War, Kobayashi became Chief of Staff of the IJN 4th Fleet and was based at Qingdao as an assistant to Rear Admiral Soemu Toyoda.

He remained in that position until March 1943 and despite having more combat experience than many of his colleagues, was assigned to personnel recruitment, munitions production, and general bureaucratic duties.

It was not until after the tide of the war started to change that Kobayashi was permitted to return to combat status with his appointment to command the IJN 4th Fleet on 1 April 1943.

After the surrender of Japan, Kobayashi was detained at Sugamo Prison in Tokyo by the SCAP authorities, and charged with command responsibility for the war crimes perpetrated by Admiral Shigematsu Sakaibara in the "Wake Island Massacre".