This page shows the winners of the cups for the 1998-99 season that are fully featured in the FCHD.
| F.A. Cup | Won by Manchester United |
| F.A. Trophy | Won by Kingstonian |
| F.A. Vase | Won by Tiverton Town |
| Football League Cup | Won by Tottenham Hotspur |
| Football League Trophy | Won by Wigan Athletic |
Other Cup competitions, not fully featured in the FCHD
| F.A. Sunday Cup | Won by Little Paxton |
| Amateur Football Alliance Senior Cup | Won by Old Finchleians |
| Welsh Cup | Won by Inter Cable-Tel |
| F.A.W. Premier Cup | Won by Barry Town |
| Scottish Cup | Won by Rangers |
| Scottish League Cup | Won by Rangers |
| Scottish Junior Cup | Won by Kilwinning Rangers |
Please credit the F.C.H.D. when using this information elsewhere