In November 1944, Shoqata Sportive Ismail Qemali was re-opened. The championship began on 16 September 1945 and the club was playing against Vllaznia. SH.S. Ismail Qemali lost 1-0. The 1945 season saw the team end in fourth place in a 6 team league. The next championship would be better for The Fleet. On 22 June 1946, the club renamed itself Klubi Sportiv Flamurtari Vlorë. The 1946 season saw Flamurtari going to the championship final after winning First Division Group B. The final was played in two legs, one in Vlorë and one in Shkodër. Flamurtari lost both matches with an aggregated score of 5–0. In 1948, Flamurtari played once again in the final, still losing to KF Partizani Tirana, 6–2 in Qemal Stafa. In 1951 the club changed its name to Puna Vlorë, but in 1958 the club used once again the name Flamurtari. In 1954 Flamurtari participated in the Spartak Cup and won the competition after beating Vllaznia 6-0 and KS Teuta and Ylli i Kuq Pogradec 2–0. After reaching twice the championship final, in 1960 made it to the Albanian Cup final. In the first round playing against Ylli i Kuq Pogradec and beating them both at home and away matches. In the second round Flamurtari would play against KS Besa Kavaje.The teams drew both matches and had to go on extra time.After 90 minutes played in Kavaje and 135 minutes played in Vlorë the two teams were still equal. Flamurtari passed the second round thanks to the corners rule: the team that had more corners would qualify. These were 8 to 5 for Flamurtari. In the third round Flamurtari played against KS Skenderbeu Korce. The first match in Vlorë ended in a 3–0 win for the home side. In Korce, in the 2nd leg match, KS Skenderbeu Korce were leading 3–0 in half-time. In the second half Flamurtari made one of the greatest comebacks in the history of Albanian football winning 4–3 in the end of the 90 minutes. In the final the team played against KS Dinamo Tirana and they lost 1–0 after a hard-fought match. The next years were almost same for the team, placed always in mid-table.
The golden years
In the 1980s Flamurtari would regained their former status as one of the big names in Albanian football. Flamurtari finished in 8th place in the 1980–81 season, but in the following season rose to second, runners-up to SK Tirana. During the season Flamurtari remained unbeaten in all matches at home in all competitions. In 1981 Flamurtari would participate for the first time in an international cup, the Balkans Cup. They played AEK Athens but they lost 3–2 in the Olympic Stadium of Athens. They finished second in their group with two wins and two losses, achieving 7–8 goals in the process. In 1983–84 Flamurtari once again reached the Albanian Cup final but lost to Tirana. In the season after, Flamurtari won the Albanian Cup. They defeated KF Partizani and thus claimed their first ever professional trophy.
In 1985–86, Flamurtari finished second in the championship losing the trophy only by goal difference to Dinamo Tirana. Finishing second in the championship, Flamurtari would play in the UEFA Cup. They were drawn against FC Barcelona. Flamurtari was eliminated after two draws (1–1 in Vlorë, 0–0 in Barcelona) thanks to the away goal rule. Flamurtari showed their strength by drawing the first match in Barcelona and taking the lead in the 26th minute in Vlorë, but FC Barcelona scored a late away goal to deny the Fleet's triumph. In that season Flamurtari managed once again to finish in 2nd place and to reach the Albanian Cup final losing on aggregate 4–3 to Vllaznia.
After a perfect season they gained the right to play for the 2nd consecutive year in the UEFA Cup. In the first round they had to play against Partizan Belgrade. After a 2–0 win in Vlorë, a result of a great Rrapo Taho and an own goal, Flamurtari were playing at Narodna Armija Stadium on 30 September 1987. Partizan were leading 2–0 until the 76th minute when Sokol Kushta scored the goal that took Flamurtari in the next round.
In the second round Flamurtari were drawn against Wismut Aue. In the first game in Aue, Flamurtari lost 0-1 being denied many times by keeper Weisflog, however in the second leg there was nothing to do for Aue as Flamurtari defeated them 2–0.
In the third round Flamurtari were drawn once again against FC Barcelona. Flamurtari won the first leg match against FC Barcelona thanks to a goal from Vasil Ruci. The enthusiasm was huge for this game, as the Stadiumi Flamurtari was crowded by an attendance of 18,500, more than double of its normal capacity of 8,500. In the second leg, Flamurtari played at Camp Nou in front of 35,000 spectators on 25 November. Flamurtari scored in the first half and the game was 0-1 for Flamurtari. The players went to the first half break with an aggregated score Flamurtari-Barcelona 2-0.
In the second half Barcelona equalised with a controversial goal. After the equaliser Flamurtari were shocked, conceding three goals in just five minutes. The match finished 4–1 for FC Barcelona, ending the longest European adventure of Flamurtari.
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 would play in the Cup Winners Cup against Lech Poznan. 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.
After the fall of communism, Flamurtari had difficult moments. Many players left the club and went to play abroad. In the 1991–92 season the club started the championship with –6 points because of financial irregularities. Flamurtari finished the Kategoria e Pare in sixth place. In the next season the club faced a huge crisis finishing the season 13th out of 16 teams. But the team improved a lot and many new players from the Youth Academy were brought in. The 1993–94 season saw Flamurtari finishing 2nd and making Stadiumi Flamurtari a fortress, winning nine and drawing four out of 13 matches played home, but away from home the team had some horrible results culminating with a 5–0 away defeat to KF Laçi. The next two seasons Flamurtari would finish in fourth place. The 1996–97 would be the best season for Flamurtari after the fall of communism. The team had a great start in the season with eight wins in the first nine games. Finishing the 1st phase of the championship in the first place, Flamurtari started the second phase while Albania was suffering the 1997 riots. Flamurtari was leading until the week the championship was suspended and the Albanian Football Association decided to play all games after in Tirana, something Flamurtari couldn't afford because of the danger. So, the Albanian Football Association decided that the championship would go to KF Tirana while Flamurtari finished in third place. The next seasons would be the worst for the team in the last 30 years with the team having its best placement in the 1998–99 season finishing 11th in a 16 team league.