After graduating from the Imperial Naval Academy with honors, in 1898 Kobayashi first served as an ensign on the corvette Hiei and by 1900 was promoted as a second lieutenant on the battleship Hatsuse.

In March 1936, in the aftermath of the February 26 Incident, Kobayashi was transferred to the Naval reserve and was appointed as Governor-General of Taiwan on 2 September 1936.

As the first military governor after a long period of the rule of civilian governors, Koobayashi followed a policy of "Japanization", believing that the colonial status should be abolished in favour of removing the distinction between the Taiwanese and the Japanese on the island and making the territory a fundamental part of the Japan homeland.

[5] This policy was termed kōminka undō (皇民化運動), which roughly meant a "campaign to transform [the conquered people] into the subjects of the emperor".

This new aggressive colonial policy also necessitated the imposition of State Shinto and bans on traditional Chinese festivals and customs.