The 1998–99 Estonian Cup () was the ninth season of the Estonian football knockout tournament. Originally, winners of the cup qualified for the 1999–2000 UEFA Cup qualifying round. The defending champion, Flora, was knocked out in the semi-final against later cup winners Levadia Maardu.
The competition culminated with the final held at Valga linnastaadion, Valga on 25 May 1999 with Levadia Maardu taking the title 3–2. Since the Tallinna Sadam were placed second in the 1998 Meistriliiga and then were merged with Levadia Maardu the UEFA Cup place was also given to the third positioned team in the league.
All in all, 40 teams took part of the competition.
First round
!colspan="3" align="center"|12 August
!colspan="3" align="center"|13 August
!colspan="3" align="center"|18 August
Second round
!colspan="3" align="center"|25 August
!colspan="3" align="center"|26 August
!colspan="3" align="center"|30 August
Third round
!colspan="3" align="center"|15 September
!colspan="3" align="center"|16 September
!colspan="3" align="center"|17 September
Fourth round
!colspan="3" align="center"|11 October
!colspan="3" align="center"|31 October
!colspan="3" align="center"|8 November
Notes 1 FC Maardu and Tallinna Sadam were merged into Levadia Maardu during the winter break and in the next round Tallinna Sadam were competed as Levadia Maardu and Levadia Maardu were competed as FC Maardu.
Quarter-finals
Semi-finals
Final
External links Official site
References Estonia Cup 1998/99 at RSSSF