| Club: | Al Ain |
| Season: | 1999–2000 |
| Chairman: | Mohammed Bin Zayed |
| Chrtitle: | President |
| Manager: | Ilie Balaci |
| League: | UAE Football League |
| League Result: | Winners |
| Cup1: | President's Cup |
| Cup2: | Federation Cup |
| Cup3: | Asian Cup Winners' Cup |
| League Topscorer: | Majid Al Owais (15) |
| Season Topscorer: | Majid Al Owais (15) |
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| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 season was Al Ain Football Club's 32nd in existence and the club's 25th consecutive season in the top-level football league in the UAE.
See main article: 1999–2000 UAE Football League.
See main article: 1999–2000 Asian Cup Winners' Cup.
Includes all competitive matches. The list is sorted alphabetically by surname when total goals are equal.
| Pos. | Player | Football League | President's Cup | Federation Cup | Asian Cup Winners' Cup | Total | |
|---|---|---|---|---|---|---|---|
| 1 | FW | 15 | 0 | 0 | 0 | 15 | |
| 2 | MF | 5 | 0 | 5 | 1 | 11 | |
| 3 | FW | 1 | 0 | 8 | 0 | 9 | |
| 4 | MF | 5 | 0 | 2 | 1 | 8 | |
| 5 | MF | 4 | 0 | 1 | 0 | 5 | |
| 6 | FW | 4 | 0 | 0 | 0 | 4 | |
| 7 | FW | 3 | 0 | 0 | 0 | 3 | |
| MF | 3 | 0 | 0 | 0 | 3 | ||
| 9 | MF | 2 | 0 | 0 | 0 | 2 | |
| FW | 0 | 0 | 2 | 0 | 2 | ||
| DF | 2 | 0 | 0 | 0 | 2 | ||
| 12 | DF | 1 | 0 | 0 | 0 | 1 | |
| MF | 1 | 0 | 0 | 0 | 1 | ||
| DF | 0 | 0 | 1 | 0 | 1 | ||
| FW | 1 | 0 | 0 | 0 | 1 | ||
| Own goals (from the opponents) | 0 | 0 | 0 | 0 | 0 | ||
| Totals | 47 | 0 | 19 | 2 | 68 |
UAE Football League[1]