It was established in the neighbourhood facilities of a local school called Mangalem, and the first team was formed with 18 teenage players.

In 1991–1992, F.K Tomori participated in the Balkans Cup but lost on aggregate to FC Oţelul Galaţi (2:4), who went on to be runners-up of the competition.

In 2000, F.K Tomori were runners-up in the championship, losing on penalty kicks against FK Tirana with the game having finished 1–1 after extra time had been played.

Tomori's biggest rivals are Naftëtari, with Kuçovë only 20 kilometres down the road and with fans of both clubs working together in the textile industry during the 1970s.

Gentian Lako was the first player to score a goal for Tomori in a UEFA CUP qualifying round.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.