Partizani were the first team to be relegated, followed by relegation/promotion playoff losers Elbasani down to the Kategoria e Dytë.
Tirana and Tomori finished the season level on points so the Albanian Football Association decided to organise a championship playoff game to determine the winner of the 1999–2000 Albanian National Championship.
The game was played at Ruzhdi Bizhuta Stadium in Elbasan and Tirana won on penalties following a 1–1 draw to retain their title.
Vllaznia and Bylis finished the season level on points so the Albanian Football Association decided to organise a playoff game to determine which side will take the Intertoto Cup place.
The game took place on 7 June 2000 in Tirana and Besa won 2–1, thanks to goals from Armand Daiu and Demneri, to earn promotion to the 2000–01 National Championship, with Elbasani being relegated down to the Kategoria e Dytë.