FC Imabari were founded in 1976 in Imabari, Ehime Prefecture, on the island of Shikoku, beginning life as a small local side called Onishi Soccer Club. The club went through several name changes and a period as a reserve team affiliated with regional rivals Ehime FC before re-establishing its independence in 2012 under the FC Imabari name.
The pivotal moment in the club's modern history came in November 2014, when Takeshi Okada — former head coach of the Japanese national team — acquired a majority stake in the club's operating company. Under his stewardship, Imabari set about building not just a competitive first team but a comprehensive football philosophy, from youth development through to the senior side. The club earned recognition as a J.League Hundred Year Vision Club in February 2016 and capped that year by winning the National Regional Football Champions League, earning promotion to the Japan Football League (JFL).
After three seasons in the JFL, Imabari secured promotion to the J3 League in 2019, becoming a fully professional club for the first time. They spent five seasons in the third tier before clinching promotion to the J2 League on 10 November 2024, finishing runners-up in J3. They marked their first J2 season in 2025 with an eleventh-place finish, and in September of that year were granted a J1 League licence, signalling ambitions to reach Japan's top flight.
The defining local rivalry — known as the Iyo Kessen — is contested against fellow Ehime Prefecture side Ehime FC, adding a fiercely regional dimension to the club's identity. Imabari now play their home matches at the purpose-built ASICS Satoyama Stadium, which opened in January 2023.