In 1990, Albania left the one-party system. Communism fell, Alija Ramiz came to power, and later Sali Berisha, and Albania slowly became a more open country. In the 1990/1991 season Flamurtari won their first and only Championship title in the history of the club. Football players of this club failed to round up a great season, and win in the Cup final where they were defeated by Partizani from Tirana after the performance of penalty-kick. With this title, Flamurtari gained the right to their first and only participation in the Champions Cup where they were eliminated in the first round by the Swedish Goteborg (1: 1, 0: 0). But only then problems began, because of the new system and openness of Albania towards Europe, many players have left the club and went abroad. In the next season, the club started with a six-point deficit because of financial problems. In the 90’ Flamurtari had very variable results. The Valona players were the closest to win the title 1996/97 season but they failed to do so mostly due to the situation in the country that dominated after the Democratic Party manipulated the election results in 1996. The disorders culminated in 1997 when there were fierce riots in major cities that were controlled by street gangs and armed "citizen groups" at one point. After these events, the club became stable, but there was no success in the Championship. Flamurtari won two more national cups in 2009 and 2014, but without much success in European competitions. In the 2016/17 season, In the last round, the club managed to fight for survival in the first league.
Football Club Flamurtari performs at the city stadium in Valona with a capacity of 16,500 places. Earlier they performed at the stadium on which their training center is today.
Flamurtari fans are called "Red Black Fleet". They the matches of their club from the eastern stand. They are considered to be the most faithful fans in the country. But today the stadium in Valona has far less audience than during the Communist.