Gozo FC spent most of its first years in the Maltese Second Division and Third Division. Gozo FC won Section B of the Second Division, the third tier of the Maltese League system, for the 1997-98 season. The following season (1998–99), they participated in the First Division and unexpectedly topped the table level with Zurrieq F.C. on 35 points. However, having a better goal difference, Zurrieq won the title. Gozo FC drew praise nonetheless, having gone from the Maltese Second Division to the Maltese Premier League in just two years.
