 Due to UNMIK, FC Prishtina were able to play in the Kosovan league system only.After Kosovo became under United Nations Administration Mission, FC Prishtina left the Serbian football league system and became part of the Football Superleague of Kosovo, which became the highest football division of Kosovo.As the club from Kosovo with most successful results in the past and the best infrastructure, FC Prishtina became dominant in the early years of the competition, and won the first two editions, in 1999–00 and 2000–01.