The 1999–2000 Copa Federación de España was the seventh staging of the Copa Federación de España, a knockout competition for Spanish football clubs in Segunda División B and Tercera División.

The Regional stages began in 1999, while the national tournament took place from November 1999 to April 2000.

Source:^[1]

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Las Rozas	0–2	Ávila	0–0	0–2
Cultural Leonesa	1–5	Racing Ferrol	0–2	1–3
Compostela B	0–6	Avilés	0–1	0–5
Noja	2–2 (a)	Lemona	0–1	2–1
Racing Santander B	2–1	Izarra	2–0	0–1
Sabadell	2–2 (a)	Logroñés B	0–1	2–1
Binéfar	3–3 (a)	Figueruelas	2–2	1–1
Arandina	4–5	Burgos	3–2	1–3
Onda	4–1	Mallorca B	1–0	3–1
Murcia	4–2	Cartagonova	3–1	1–1
Elche	7–2	Águilas	2–1	5–1
Jerez	0–1	Linense	0–0	0–1
Las Palmas B	1–4	Universidad de Las Palmas	0–1	1–3
Lanzarote	3–2	Cádiz	1–1	2–1
Villarrobledo	w.o.	Levante

• Lucentino received a bye.

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Noja	3–2	Avilés	3–1	0–1
Racing Ferrol	1–2	Racing Santander B	1–0	0–2
Villarrobledo	1–4	Burgos	1–2	0–2
Ávila	5–1	Figueruelas	2–1	3–0
Onda	3–4	Elche	1–1	2–3
Sabadell	3–2	Murcia	1–1	2–1
Lucentino	3–3 (a)	Linense	2–2	1–1
Lanzarote	3–0	Universidad de Las Palmas	0–0	3–0

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Noja	1–1 (a)	Racing Santander B	1–1	0–0
Sabadell	3–2	Lanzarote	2–1	1–1
Linense	3–3 (p)	Elche	1–2	2–1
Burgos	5–4	Ávila	5–1	0–3

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Burgos	1–4	Elche	1–1	0–3
Racing Santander B	1–4	Sabadell	1–0	0–4

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Sabadell	3–3 (a)	Elche	2–0	1–3 (a.e.t.)

• 2000–2009 Copa Federación results
• Asturias tournament results