The EHF European Cup Winners' Cup in 1998/99 took part in 35 handball club teams that had qualified for the competition in their home countries in the previous season in the cup competition. It was the 24th edition of the European Cup Winners' Cup. The cup games began on September 11, 1998 and ended with the second final game on April 17, 1999. In the final, the Spanish club Ademar León was able to prevail against the defending champion from Spain CB Santander .
The competition started with two games in one elimination round. The winners advanced to the sixteenth finals, in which other, higher ranked teams entered. All rounds including the final were carried out in a knockout system with a return leg. The winner of the final was the European Cup Winner of the 1998/99 season.
Elimination round
The home and return games took place on 28/29/30. August.
total
First leg
Return leg
HC Mamuli Tbilisi Georgia 1990
43: 55
Belarus 1995SKAF Minsk
26:27
17:28
HC Kehra Tallinn Estonia
42: 49
LuxembourgHandball Esch
20:21
22:28
RK Bosna VisokoBosnia and Herzegovina 1992
60 : 42
Cyprus 1960 PES Strovolou Nicosia
30:23
30:19
Sixteenth finals
The home and away games took place between September 25, 1993 and October 3, 1993.
total
First leg
Return leg
RK Partizan BelgradeYugoslavia Federal Republic 1992
46 : 40
Hungary Pestszentlörinc Elektromos SE
25:20
21:20
Olse Merksem Belgium
36: 57
FranceSporting Toulouse 31
17:29
19:28
Otterup HK Denmark
41: 59
SpainCantabria Santander
23:26
18:33
Šiauliai Universitetas Lithuania
31: 71
SpainAdemar León
12:32
19:39
IFK Skövde HK Sweden
23: 32
North MacedoniaVardar Skopje
23:22
0:10
Wisla Plock Poland
60: 63
NorwayIL Runar Sandefjord
34:29
26:34
Çankaya Belediyesi AnkaraTurkey
54 : 49
Russia Istochnik Rostov
26:24
28:25
Fibrex Săvineşti Romania
38: 66
GermanyTV Niederwürzbach
21:37
17:29
Handball Esch Luxembourg
46: 57
ItalyACSI Haenna
24:26
22:31
Sporting Lisbon Portugal
42: 46
SlovakiaTJ VSŽ Košice
24:22
18:24
RK Bosna Visoko Bosnia and Herzegovina 1992
35: 37
GreeceAthinaikos Athens
20:15
15:22
HC BrovaryUkraine
51 : 40
Bulgaria HK Lokomotiv Varna
31:19
20:21
SKAF Minsk Belarus 1995
39: 43
NetherlandsHV Aalsmeer
24:24
15:19
TSV St. Otmar St. Gallen Switzerland
54: 59
SloveniaRK Velenje
31:26
23:33
Dukla PragueCzech Republic
60 : 51
Croatia RK Đakovo
34:30
26:21
Maccabi Rechovot Israel
42: 45
AustriaUHC Tulln
19:26
23:19
Round of 16
The first legs took place on 30./31. October 1993 and the second leg on 6./7. November 1993.
total
First leg
Return leg
Vardar SkopjeNorth Macedonia
53 : 51
Slovenia RK Velenje
29:23
24:28
RK Partizan BelgradeYugoslavia Federal Republic 1992
61 : 52
Slovakia TJ VSŽ Košice
35:27
26:25
IL Runar SandefjordNorway
71 : 45
Italy ACSI Haenna
38:18
33:27
Çankaya Belediyesi AnkaraTurkey
45 : 44
Ukraine HC Brovary
24:17
21:27
TV NiederwürzbachGermany
65 : 50
Czech Republic Dukla Prague
36:21
29:29
Sporting Toulouse 31France
51 : 39
Netherlands HV Aalsmeer
27:18
24:21
Ademar LeónSpain
59 : 34
Greece Athinaikos Athens
30:14
29:20
Cantabria SantanderSpain
47 : 35
Austria UHC Tulln
21:14
26:21
Quarter finals
The first legs took place on 19/22/23. January 1994 and the second leg on 26./29. November 1994.
total
First leg
Return leg
IL Runar Sandefjord Norway
49: 55
SpainCantabria Santander
24:24
25:31
Çankaya Belediyesi Ankara Turkey
42: 60
SpainAdemar León
26:27
16:33
TV Niederwürzbach Germany
48: 50
Yugoslavia Federal Republic 1992RK Partizan Belgrade
28:22
20:28
Vardar SkopjeNorth Macedonia
50 : 46
France Sporting Toulouse 31
26:19
24:27
Semifinals
The first legs took place on March 23, 1994 and the second legs on 6/7. April 1994.
total
First leg
Return leg
Vardar Skopje North Macedonia
47: 64
SpainAdemar León
27:29
20:35
RK Partizan Belgrade Yugoslavia Federal Republic 1992
43: 45
SpainCantabria Santander
26:23
17:22
final
The first leg took place on April 10, 1999 in Santander and the second leg on April 17, 1999 in León . The encounter was the same as in the Spanish Cup final last year. Cantabria Santander won there, but was already qualified as defending champion for the European Cup Winners' Cup, which is why Ademar León also took part.