The 1999–2000 Estonian Cup () was the tenth season of the Estonian football knockout tournament. Originally, winners of the cup qualified for the 2000–01 UEFA Cup qualifying round. The defending champion, Levadia Maardu, was successfully defend the title, after winning the final 2–0, which was held at Pärnu Kalevi staadion, Pärnu on 28 May 2000. Since the Levadia Maardu also win the 1999 Meistriliiga, the UEFA Cup places were moved to second and third positioned team in the league.
All in all, 31 teams took part of the competition.
First round
Second round
Third round
Notes 1 Lantana were withdraw from the competition during the winter break and were replaced by Valga. 2 Lelle SK were renamed to Tervis Pärnu during the winter break.
Quarter-finals
Semi-finals
Final
External links Official site
References Estonia Cup 1999/2000 at RSSSF