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The 1998–99 Copa del Rey was the 97th staging of the Copa del Rey.

The competition started on 1 September 1998 and concluded on 26 May 1999 with the Final, held at the Estadio La Cartuja in Sevilla.

First round

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Cádiz CF	4–3	Granada CF	2–2	2–1
Terrassa FC	2–4	Levante UD	1–1	1–3
Talavera CF	3–1	CD Toledo	1–1	2–0
Palamós CF	2–4	Benidorm CF	1–1	1–3
CD Lealtad	2–4	Sporting de Gijón	2–1	0–3
CD Lalín	1–4	UD Las Palmas	1–0	0–4
Cultural Leonesa	3–3	CD Numancia	2–2	1–1
SD Noja	0–4	CA Osasuna	0–1	0–3
Elche CF	2–1	Hércules CF	1–0	1–1
UE Lleida	4–1	Águilas CF	3–0	1–1
UB Conquense	0–4	Albacete Balompié	0–3	0–1
Real Jaén	1–3	Sevilla FC	1–1	0–2
Algeciras CF	1–3	Recreativo de Huelva	1–0	0–3
Xerez CD	2–3	Málaga CF	2–1	0–2
Universidad de Las Palmas CF	2–3	SD Compostela	1–1	1–2
SD Beasain	1–1	SD Eibar	0–0	1–1
CD Calahorra	1–3	CD Ourense	1–1	0–2
CD Móstoles	1–4	CD Badajoz	1–2	0–2
Jerez CF	4–3	Rayo Vallecano	2–2	2–1
UD San Sebastián de los Reyes	2–2	CP Mérida	1–0	1–2

Second Round [Sep 24; Oct 7]

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Elche CF	2–3	Benidorm CF	1–1	1–2
SD Beasain	3–1	CD Logroñés	3–1	0–0
CD Tropezón	0–4	UE Lleida	0–0	0–4
Barakaldo CF	2–5	CD Numancia	0–2	2–3
CD Binéfar	0–2	CA Osasuna	0–0	0–2
CD Ourense	0–0 (3–4)	Sporting de Gijón	0–0	0–0
Jerez CF	3–1	Recreativo de Huelva	2–1	1–0
Cartagonova CF	1–6	Levante UD	0–2	1–4
UD San Sebastián de los Reyes	4–3	Albacete Balompié	2–1	2–2
CP Cacereño	2–6	Sevilla FC	0–4	2–2
Talavera CF	1–1	CD Leganés	0–0	1–1
Cádiz CF	1–6	Málaga CF	1–3	0–3
UD Las Palmas	2–1	SD Compostela	2–0	0–1
AD Ceuta	1–3	CD Badajoz	0–1	1–2

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
UD Las Palmas	2–2	Deportivo Alavés	0–0	2–2
Levante UD	0–0 (4–1)	CF Extremadura	0–0	0–0
Sevilla FC	2–0	UD Salamanca	0–0	2–0
UD San Sebastián de los Reyes	2–4 (aet)	CD Tenerife	2–0	0–4
Sporting de Gijón	3–3	Real Zaragoza	1–1	2–2
Málaga CF	3–5	Real Valladolid	1–2	2–3
Talavera CF	0–4	Villarreal CF	0–1	0–3
CD Numancia	1–2 (aet)	Racing de Santander	0–1	1–1
Jerez CF	2–6	RC Deportivo de La Coruña	1–3	1–3
CD Badajoz	4–1	Real Oviedo	3–1	1–0
UE Lleida	1–3	CA Osasuna	1–1	0–2
SD Beasain	0–1	Benidorm CF	0–0	0–1

Fourth Round [Dec 16; Jan 13]

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Deportivo de La Coruña	2–1	Sporting de Gijón	1–1	1–0
UD Las Palmas	0–1	Levante UD	0–1	0–0
Racing de Santander	2–1	CA Osasuna	2–0	0–1
Real Valladolid	2–2 (11–10)	CD Badajoz	1–1	1–1
Villarreal CF	5–3	Sevilla FC	2–2	3–1
CD Tenerife	2–2	Benidorm CF	2–2	0–0

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Real Madrid	4–0	Villarreal CF	2–0	2–0
RCD Espanyol	6–4	Real Valladolid	4–2	2–2
RC Celta de Vigo	1–2	RC Deportivo de La Coruña	0–1	1–1
Athletic Bilbao	2–3	Racing de Santander	2–2	0–1
Levante UD	0–4	Valencia CF	0–3	0–1
Benidorm CF	0–4	FC Barcelona	0–1	0–3
Real Sociedad	2–2	Atlético de Madrid	1–2	1–0
Real Betis	0–2	RCD Mallorca	0–1	0–1

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Racing de Santander	2–7	Real Madrid	2–6	0–1
Atlético de Madrid	6–2	RCD Espanyol	2–1	4–1
RCD Mallorca	1–2	RC Deportivo de La Coruña	1–1	0–1
FC Barcelona	5–7	Valencia CF	2–3	3–4

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Valencia CF	7–2	Real Madrid CF	6–0	1–2
Atlético de Madrid	1–0	RC Deportivo de La Coruña	0–0	1–0

26 June 1999

21:30 CEST

Atlético Madrid	0–3	Valencia
	Report	López 22', 81' Mendieta 33'

Attendance: 45,000