After Montenegrin independent, Sutjeska became a member of the Montenegrin First League. The first significant win at the time was when the team participated the Montenegrin Cup 2006-07. They made it to the finals however, they lost to FK Rudar (1-2). As a third-placed team in the 2008-09 season Sutjeska was the first team to play as a team in the UEFA Europa League, but they were eliminated by FC Partizan Minsk from Belarus (1-1 1-1; 1-1).).
The first national title in the club's history, FK Sutjeska won on the 2012-13 season, scoring five more points than their rivals of the past FK Buducnost. FK Buducnost. In the course of that season, FK Sutjeska home games were watched by over 7000 fans this was the highest attendance since the 80s. As Sutjeska was a Montenegrin winner, Sutjeska participated in UEFA Champions League 2013-14 qualifying matches and was eliminated during the 2nd round against Moldavian team FC Sheriff.
The 2013-14 season saw FK Sutjeska became first Montenegrin club to defend a national title last season. They took the title following the long and intense race against FK Lovcen and gained a chance to take part in UEFA Champions League. On the second qualifying round FK Sutjeska again failed against the well-known rival, FC Sheriff.
Another year one more time in Europe, Sutjeska played in the 2015-16 UEFA Europa League, with two thrilling matches against Hungary's Debreceni VSC (2-0; 0-3).
In the 2016-17 season, FK Sutjeska made a new record with this one, this time at the Montenegrin Cup. This was the 2nd time in their the history of the tournament they took part in the Cup finals. However, this time, they took the trophy by winning against OFK Grbalj (1-0).
From 2017to 2018, FK Sutjeska played two impressive seasons, winning two new championships and a great performance at European competitions. In the 2017-18 season, helmed by the Niksic-born coach Nikola Rakojevic, they won the title by scoring an extra 22 points over their top opponents and runners-up from FK Buducnost. However, Sutjeska player Igor Ivanovic became the highest scoring player during the season. The following time, FK Sutjeska, again along with head coach Rakojevic was able to defend the title again, but this time with a much more intense battle in the battle with FK Buducnost. In the following month, the team from Niksic had a good performance in the 2019.20 Champions League, as they defeated Slovan Bratislava in the first stage of qualifying. They will be eliminated at the next stage, which is against APOEL.
After three seasons that ended with domestic trophies FK Sutjeska performances on season 2019-20 were weaker, which means they were runners-up. In the course of the season, they scored the biggest away win in the history of the Montenegrin Derby, against FK Buducnost in Podgorica (4-1). In addition they were also among the semifinalists in the Montenegrin Cup, but the tournament was halted because of COVID-19.