The 2006–07 Estonian Cup () was the 17th season of the Estonian football knockout tournament. Originally, winners of the cup qualified for the 2007–08 UEFA Cup first qualifying round. The defending champion, TVMK, was knocked out in the semi-final against Levadia.
The competition culminated with the final held at Kadriorg Stadium, Tallinn on 15 May 2007 with Levadia taking the title 3–0. Since the Levadia also win the 2006 Meistriliiga, the UEFA Cup places were moved to second and third positioned team in the league.
All in all, 64 teams took part of the competition.
First round
!colspan="3" align="center"|1 August
!colspan="3" align="center"|2 August
!colspan="3" align="center"|3 August
!colspan="3" align="center"|7 August
Second round
!colspan="3" align="center"|29 August
!colspan="3" align="center"|30 August
!colspan="3" align="center"|5 September
!colspan="3" align="center"|6 September
!colspan="3" align="center"|7 September
Third round
!colspan="3" align="center"|8 November
!colspan="3" align="center"|9 November
!colspan="3" align="center"|11 November
Notes 1 Maag were merged with Tammeka during the winter break and were renamed to Maag Tammeka.
Quarter-finals
Semi-finals
Final
External links Official site
References Estonia Cup 2006/07 at RSSSF