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The 1999–2000 Asian Cup Winners' Cup was the tenth edition of association football competition run by the Asian Football Confederation specifically for its members cup holders.

First round

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Esteghlal	15–0	Homenmen	7–0	8–0
Al Arabi	(w/o)¹	Al-Zawraa
Al Ittihad	1–4	Al Rayyan	0–2	1–2
Al Jaish	2–2 (a)	Al Ain	0–1	2–1
Kaisar Hurricane	3–3 (4–3 p)	Khujand	3–0	0–3
Al Ahli	bye
Al Ittihad	bye
Navbahor Namangan	bye

¹ Al Arabi withdrew

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
New Radiant	1–4	Công An Thành Phố Hồ Chí Minh	1–3	0–1

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Al Ittihad	2–1	Esteghlal	1–0	1–1
Al-Zawraa	5–4	Al Rayyan	5–2	0–2
Al Ahli	3–0	Al-Jaish	1–0	2–0
Kaisar Hurricane	2–3	Navbahor Namangan	2–2	0–1

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Shanghai Shenhua	0–2	Shimizu S-Pulse	0–0	0–2
Sembawang Rangers	(w/o)¹	Anyang LG Cheetahs
Công An Thành Phố Hồ Chí Minh	1–4	South China	1–1	0–3
Bangkok Bank	6–0	Persebaya Surabaya	5–0	1–0

¹ Sembawang Rangers withdrew before 1st leg

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Al Ittihad	1–2	Al-Zawraa	1–2	0–0
Al Ahli	6–3¹	Navbahor Namangan	6–1	0–2

¹ Al Ahli withdrew for the semifinals, and were replaced by Navbahor Namangan; Al Ahli were banned for one year from Asian club competitions.

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Shimizu S-Pulse	5–2	Anyang LG Cheetahs	3–1	2–1
South China	3–5	Bangkok Bank	3–2	0–3

13 April 2000

13 April 2000

Al-Zawraa	2–1	Navbahor Namangan
Ahmed Sabie 45' Mohammed 102'		Sherzod Nazarov 36'

15 April 2000

Bangkok Bank	3–1	Navbahor Namangan
Apichart Thaweechalermdit 4' (pen.) Apiruck Sriaroon 36' Nawee Hatihakreangkrai 38'

15 April 2000

Shimizu S-Pulse	1–0	Al-Zawraa
Shohei Ikeda 74'