The winner of the Bosnian Cup as well as the runner-up and third placed team on the table starts from the first qualifying round of the UEFA Conference League.

After the breakup of Yugoslavia, and following proclamation of independence in late winter 1992, many clubs from Bosnia and Herzegovina left the Yugoslav First League.

Only football on a territory under the control of the then Republic of Bosnia and Herzegovina institutions and auspices of N/FSBiH, at the time consequently with Bosniak majority, apart from a brief competition for the 1994–95 season (won by Čelik Zenica), came to a standstill.

Since FIFA and UEFA showed support only for the association operating under patronage of the official and internationally recognized state institutions, during the war and prior to the Dayton Agreement, as well as after its signage, they endorsed unification of all three organizations as the N/FSBiH.

Next season the play-off was resumed for the last time prior to the full and final agreement on a unified N/FSBiH and its competition, the Bosnian Premier League (Premijer Liga), in the fall of 2000.

[2] In May 2024, the N/FSBiH decided that the number of teams competing in the Premier League will be reduced to ten, starting from the 2025–26 season.

[6] Forty clubs have played in the Premier League of Bosnia and Herzegovina from its inception in 2000, up to and including the 2024–25 season.

The second time a Bosnian club moved into the last qualifying round of the UEFA Champions League was FK Sarajevo in 2007–08, when they lost to Dynamo Kyiv 0–4 on aggregate, after going over Maltese Marsaxlokk and Belgian side Genk.

Sarajevo made it again in the 2014–15 UEFA Europa League, playing all the way to the play-off round where they lost to Borussia Mönchengladbach.

In the 2020–21 UEFA Europa League season, Sarajevo once again played in the play-off round, this time losing to Celtic.

After getting eliminated from the 2022–23 UEFA Champions League first qualifying round, Zrinjski Mostar made it to the 2022–23 UEFA Europa Conference League play-off round, where they got eliminated by Slovak club Slovan Bratislava following a penalty shoot-out, missing out on a chance to play in the group stage.

[12] This result also meant that they became the first ever Bosnian side to win a game in a UEFA club competition group stage.

[13] The team lost their next four games in the group, before ending their European campaign with a home draw against Aston Villa on 14 December 2023.