The 2003–04 Estonian Cup () was the 14th season of the Estonian football knockout tournament. Winners of the cup qualified for the 2004–05 UEFA Cup first qualifying round.
The competition culminated with the final held at Kadriorg Stadium, Tallinn on 20 May 2004 with Levadia taking the title 3–0 against the defending champion TMVK.
All in all, 20 teams took part of the competition.
First round
!colspan="3" align="center"|9 September
Second round
!colspan="3" align="center"|8 November
!colspan="3" align="center"|9 November
Notes 1 Lootus were renamed to Alutaguse Lootus during the winter break. 2 Levadia Maardu were relocated to Tallinn and were renamed to Levadia Tallinn during the winter break. 3 Levadia Tallinn were renamed to Levadia II Tallinn during the winter break.
Quarter-finals The first legs were played between 18 and 20 March 2004, and the second legs on 14 and 15 April 2004.
Semi-finals The first legs were played on 29 April 2004, and the second legs on 12 May 2004.
Final
External links Official site
References Estonia Cup 2003/04 at RSSSF