1999–2000 EHF Women's Cup Winners' Cup

The 1999–2000 EHF Women's Cup Winners' Cup was the twenty-fourth edition of EHF's competition for women's handball national cup champions. It ran from October 1, 1999, to May 28, 2000.

1997 Champions League champion Mar Valencia became the first Spanish team to win the Cup Winners' Cup, defeating 1988 and 1989 champion Kuban Krasnodar in the final.

Results

	Preliminary round October 1–10, 1999						Round of 16 October 30 – November 7, 1999						Quarterfinals March 18–26, 2000						Semifinals April 22–30, 2000						Final May 20–28, 2000
	Iskra Partizánske	22	22	44
	Kuban Krasnodar	23	26	49			Kuban Krasnodar	35	34	69
	RK Skopje	13	15	28			LC Brühl	24	18	42
	LC Brühl	28	25	53									Kuban Krasnodar	29	20	49
													Nordstrand IF	18	16	34
							Nordstrand IF	35	30	65
	UHC Stockerau	38	38	76			UHC Stockerau	19	23	42
	Kolkheti Poti	14	18	32															Kuban Krasnodar	26	20	46
																			Spartak Kyiv	15	30	45
							Larvik HK	36	14	50
	Üsküdar Belediyesi	16	15	31			Spartak Kyiv	24	28	52
	Spartak Kyiv	45	38	83									Spartak Kyiv	31	26	57
	Maccabi Holon	21	13	34									TV Lützellinden	30	29	59
	TV Lützellinden	31	44	75			TV Lützellinden	37	39	76
	Sporting Neerpelt	36	31	67			Sporting Neerpelt	15	10	25
	AC Latsia	15	24	39																					Kuban Krasnodar	24	30	54
	Lokomotiv Plovdiv	22	25	47																					Mar Valencia	31	31	62
	Oţelul Galaţi	26	24	50			Oţelul Galaţi	31	27	58
	OFN Ionias	21	24	45			OFN Ionias	20	24	44
	SK Ulbroka	17	20	37									Oţelul Galaţi	18	22	40
	Ikast Bording	27	23	50									Ikast Bording	20	23	43
	Napredak Kruševac	22	24	46			Ikast Bording	24	28	52
	Olimpija Ljubljana	28	24	52			Olimpija Ljubljana	23	20	43
	Cercle Nîmes	15	22	37															Ikast Bording	28	21	49
	SV Nieuwegein																		Mar Valencia	25	31	56
	Kras Zagreb			w/o			Kras Zagreb	28	27	55
	Porto Salvo	26	17	43			Start Elblag	29	24	53
	Start Elblag	34	40	74									Kras Zagreb	25	25	50
	HC Rimini												Mar Valencia	29	32	61
	Mar Valencia			w/o			Mar Valencia	29	23	52
	Győri Graboplast	48	33	81			Győri ETO	21	27	48
	Željezničar Sarajevo	12	13	25