The passion and desire for the game of football was integrated into the hearts of local citizens and patriots since the early years of
World War I.
Rrogozhinë, being neighbours to
Kavajë, a city with a long tradition in football on a national level, knew how to use this experience to its own advantage by forming initially an amateur level team which would later go on to compete in the second division of Albanian football. The very first match in club history was a friendly between
Besa in 1934 which ended in a 1–7 loss. Mustafa Cara, a student of agronomy in
Bari, Italy who had returned home for vacation (he was a player for
Fidelis Andria, a Serie B club in Italy at the time), scored 5 goals for Besa. Following the liberation of the country after
World War II, the league structure changed by allowing only district level teams to compete in the top two divisions. This made it difficult for Rrogozhinë, a locality at the time, to compete on a national level. Egnatia had one season in the top tier of Albanian football after winning promotion in summer 2004. They were relegated after their first season, with
Alfred Ferko succeeding
Hysen Dedja and Petrit Haxhia as first team coach during the season.
Recent years Egnatia were promoted back to the top flight of Albanian football, the
Kategoria Superiore, for the second time in their history on 2 May 2021, following a 1–0 victory over local rivals
Besa Kavajë in the Promotion Round of the
2020–21 Kategoria e Parë. Under head coach
Gugash Magani, they finished top of Group B during the regular season and qualified for the Promotion Round, where they also finished top, securing their place in the championship final held on 21 May 2021 against the winners of Group A,
Dinamo Tirana, where they won 1–0 through a stoppage-time winner from
Ndriçim Shtubina. In 26 May 2024, Egnatia won their first title of the
Kategoria Superiore, after beating
Partizani in the final. ==Stadium==