The 1998–99 EHF Women's Cup Winners' Cup was the 23rd edition of EHF's competition for women's handball national cup champions. It ran from October 3, 1998, to May 15, 1999.

Defending champion Bækkelagets SK won again the competition, beating Ferrobús Tortajada in the final. For the first time in the Cup Winners' Cup's history no team from the former Eastern Bloc or former Yugoslavia reached the final.^[1]

	Preliminary round October 3–11, 1998						Round of 16 November 7–15, 1998						Quarterfinals February 27 – March 7, 1999						Semifinals April 10–17, 1999						Final May 8–15, 1999
	Colégio de Gaia	15	15	30
	Kuban Krasnodar	36	32	68			Kuban Krasnodar	28	34	62
	LC Brühl	41	32	73			LC Brühl	22	28	50
	HB Dudelange	19	10	29									Kuban Krasnodar	23	19	42
													ASPTT Metz	14	30	44
							TV Lützellinden	29	17	46
	Zagłębie Lubin	21	18	39			ASPTT Metz	24	27	51
	ASPTT Metz	22	30	52															ASPTT Metz	17	22	39
																			Bækkelagets SK	17	28	45
							Bækkelagets SK	32	28	60
	Slavia Prague	22	23	45			Slavia Prague	21	23	44
	Anadolu Üniversitesi	15	27	42									Bækkelagets SK	32	22	54
	HC Struzanka	12	10	22									Larvik HK	19	23	42
	Larvik HK	38	37				Larvik HK	33	24	57
	Herz Ferencváros	32	30	62			Herz Ferencváros	23	33	56
	SEW Zeeman	12	17	29																					Bækkelagets SK	26	24	50
	Maccabi Holon	20	12	32																					Ferrobús Tortajada	13	22	35
	Spartak Kyiv	30	33	63			Spartak Kyiv	30	27	57
	SSV Dornbirn	19	13	32			Vikas Vilnius	21	26	47
	Vikas Vilnius	31	34	65									Spartak Kyiv	13	21	34
	RSVSMRUOR Minsk	24	23	47									Ferrobús Tortajada	24	17	41
	Silcotub Zalău	33	32	65			Silcotub Zalău	15	22	37
	HC Gorazde	4	5	9			Ferrobús Tortajada	27	25	52
	Ferrobús Tortajada	43	40	83															Ferrobús Tortajada	25	21	46
																			Frederiksberg IF	20	20	40
							Kras Zagreb	42	39	81
	OFN Ionias	20	15	35			Aves Burgas	18	15	33
	Aves Burgas	18	23	41									Kras Zagreb	24	23	47
	Frederiksberg IF	36	31	67									Frederiksberg IF	31	22	53
	Duvanska Niš	23	17	40			Frederiksberg IF	32	20	52
	DeGasperi Enna	17	20	37			Olimpija Ljubljana	21	30	51
	Olimpija Ljubljana	30	26	56