At first clubs from Federation of Bosnia and Herzegovina entity First League of Herzeg-Bosnia and First League of Bosnia and Herzegovina played in playoff for champion at the end of the season, while football organization from Republika Srpska entity refused to participate for the time being, indeed until two years after creation of Premier League of Bosnia and Herzegovina and 2002–03 season.
After a breakup of Yugoslavia Bosnia and Herzegovina proclaimed independence in late winter 1992, and already in April same year N/FSBiH applied for membership with FIFA and UEFA.
In 1993 Bosnian Croats launched the First League of Herzeg-Bosnia in which only Croatian clubs competed on parochial scale within the limits of West Herzegovina and few other enclaves.
Only football on a territory under the control of 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 season 1994–95 (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 Dayton Peace Agreement as well as after its signedge, they endorsed unification of all three organizations as N/FSBiH.
Idea was that playoff under unified N/FSBiH auspices should bring together clubs competing under three separate organizations for the first time but was rejected by Serb association, leaving clubs from Croat football association and N/FSBiH participating playoff for the seasons 1997–98 and 1999–00, while 1998–99 playoff was canceled due to Croat's association hesitation on the decision on which stadiums games should be played.
Next season playoff was resumed for the last time prior to full and final agreement on unified N/FSBiH and its competition, Premier League BiH (Premijer Liga), in the fall 2000.