On March 1, 1960 the squadron was formed at Komaki Air Base as part of the 3rd Air Wing. It moved to Chitose Air Base in 1961 and did Quick Reaction Alert duty for two years, until December 1963. The following year the 203rd Squadron was formed flying the Lockheed F-104 Starfighter.
It was disbanded on October 1, 1968, the same day as the 101st Squadron. At that time the type of aircraft operated by a Japanese fighter squadron was linked to the type of aircraft operated. Squadrons 101-105 were F-86D squadrons.