Their first honour was the 1995-96 Maltese Second and Third Division Knock-Out, when Gozo FC ran out 5-2 winners against Għaxaq in a match played at the National Stadium.

Gozo FC won Section B of the Second Division, the third tier of the Maltese League system, for the 1997-98 season.

The 1999-2000 season is considered the high water mark in the short history of Gozo FC.

They drew against Maltese powerhouse Sliema Wanderers, and even though their tie was played at home, they could not match up to their more illustrious opponents and suffered a 6-1 defeat.

When the division was split into two, Gozo FC occupied eighth position with 14 points from 18 outings.

Given they were considered the hot favourites for relegation, their performances were above expectations and they never suffered a humiliating defeat.

While from 9 away fixtures they only collected five points, a win against Pieta Hotspurs and two draws with Naxxar Lions and Zurrieq respectively, at home they proved to be a difficult bone to crack down.

In the whole season Gozo FC scored a total of 22 goals and conceded only 39, the fourth best defence in the premier division.

In the 2005/2006 Gozo FC showed some good performances and they ended their campaign in a comfortable sixth position.

This time, Gozo FC were in class of their own and proved too strong for their opponents and topped the Third Division Section B.

This entitled them for a promotion play-off against Żebbuġ Rangers which won their respective division that is Section A.