The 1998–99 Asian Cup Winners' Cup was the ninth edition of association football competition run by the Asian Football Confederation (AFC) specifically for the winners of domestic cup competitions in AFC members nations.
First round
West Asia
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
Kazma 
|
5–2 |  Al Wahda
|
2–0 | 3–2 |
Al Ahli 
|
0–3 |  Al Talaba
|
0–0 | 0–3 |
PAS 
|
10–3 |  Al-Seeb
|
10–1 | 0–2 |
Al Ahli 
|
(w/o)1 |  Al Nejmeh
|
||
Khujand 
|
2–5 |  Pakhtakor
|
1–1 | 1–4 |
Nisa Aşgabat 
|
2–1 |  Kaisar Kzyl-Orda
|
1–0 | 1–1 |
Al Ittihad 
|
bye | |||
| Al Nassr
|
bye |
1 Al Nejmeh withdrew.
East Asia
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
Sinthana 
|
5–2 |  Woodlands Wellington
|
4–1 | 1–1 |
Ho Chi Minh City Customs 
|
2–5 |  Sarawak
|
1–2 | 1–3 |
Chunnam Dragons 
|
(w/o)1 |  Police SC
|
||
Salgaocar 
|
1–4 |  Beijing Guoan
|
1–0 | 0–4 |
Mahendra Police 
|
0–2 |  New Radiant
|
0–0 | 0–2 |
Happy Valley 
|
(w/o)2 |  PIA
|
||
Yangon City Development 
|
bye3 | |||
Kashima Antlers 
|
bye |
1 Police SC withdrew.
2 PIA FC withdrew.
3 Yangon City Development had been drawn against the representatives of Indonesia, where the 1997/98 season was abandoned and the cup cancelled due to political and economic turmoil in the country.
Second round
West Asia
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Kazma
|
4–2 | Al-Nassr
|
3–0 | 1–2 |
| PAS
|
1–2 | Al Talaba
|
0–1 | 1–1 |
| Al Ahli
|
1–7 | Al Ittihad
|
0–0 | 1–7 |
| Nisa Aşgabat
|
5–6 | Pakhtakor
|
5–0 | 0–6 |
East Asia
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Yangon City Development
|
0–4 | Sarawak
|
0–1 | 0–31 |
| New Radiant
|
4–6 | Happy Valley
|
3–1 | 1–5 |
| Sinthana
|
1–11 | Kashima Antlers
|
1–2 | 0–9 |
| Beijing Guoan
|
0–4 | Chunnam Dragons
|
0–2 | 0–2 |
1 Yangon City Development were unable to field a team for the second leg to player illness.
Quarterfinals
West Asia
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Kazma
|
(w/o)1 | Al Talaba
|
||
| Al Ittihad
|
4–0 | Pakhtakor
|
3–0 | 1–0 |
1 Kazma withdrew.
East Asia
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Happy Valley
|
1–7 | Chunnam Dragons
|
0–3 | 1–4 |
| Sarawak
|
2–14 | Kashima Antlers
|
2–4 | 0–10 |
Semifinals
| Al Talaba | 1–3 | Al Ittihad |
|---|---|---|
Qahtan Chathir Drain  36' |
Mohammed Al Sahafi 20' Dalian Atkinson 25' Ahmed Bahja 90' |
Kashima Antlers  | 1–4 |  Chunnam Dragons |
|---|---|---|
| Yutaka Akita 12' |
Roh Sang-Rae 33', 86' Kim Jong-hyun 48' Lim Kwan-Sik 66' |
Third place match
Final
| Al Ittihad | 3–2 (a.e.t.) | Chunnam Dragons |
|---|---|---|
Ahmed Bahja 10' (pen.)  105' Mohammed Noor 84' |
Roh Sang-Rae 14', 70' |
Referee: Ali Bujsaim ( United Arab Emirates)