In the same season Flamurtari went all the way to win the Albanian Cup, after beating KF Partizani, 1–0, and securing their second cup title. In 1989 Flamurtari played in the Cup Winners Cup against Lech Poznań. After two games Flamurtari was eliminated by losing both home and away matches, 4–2 on aggregate. In the Kategoria Superiore the team finished in the third place. Just a year after Flamurtari lifted for the first time in their history the Kategoria Superiore title. After some stunning results during the season (including beating runners-up Partizani 3–0 and third-place Vllaznia 5–2), they won the championship with a six-point lead. In the same year they would win also the Albanian Supercup.