The club started out as a youth team, but in 1992 a senior squad was founded and it entered the Finnish league system at the fourth level (third division Kolmonen).

The squad was strengthened with new players, and in 1996, as both of Turku's better teams were now playing in the Veikkausliiga, the club's attendance records were broken with 8,200 spectators in the local derby between Turun Palloseura (TPS) and Inter.

Since then the club has consistently finished between 7th and 4th in the league, and maintained a steady inflow of foreign players as well as young starlets from its own youth academy.

During the 2006 season Inter sacked their manager Kari Virtanen and hired new coach, Dutchman Rene van Eck.

In 2008 Inter led the league since early season and clinched their first Finnish championship title after winning against FF Jaro in their final game.