The 1998–99 Japan Ice Hockey League season was the 33rd season of the Japan Ice Hockey League. Six teams participated in the league, and Kokudo Ice Hockey Club won the championship.
| Team | GP | W | L | T | GF | GA | Pts | |
|---|---|---|---|---|---|---|---|---|
| 1. | Kokudo Ice Hockey Club | 40 | 31 | 8 | 1 | 182 | 93 | 63 |
| 2. | Oji Seishi Hockey | 40 | 21 | 18 | 1 | 147 | 142 | 43 |
| 3. | Seibu Tetsudo | 40 | 26 | 12 | 2 | 165 | 122 | 54 |
| 4. | Nippon Paper Cranes | 40 | 18 | 18 | 4 | 138 | 147 | 40 |
| 5. | Sapporo Snow Brand | 40 | 11 | 26 | 3 | 120 | 162 | 25 |
| 6. | Furukawa Ice Hockey Club | 40 | 6 | 31 | 3 | 100 | 186 | 15 |
| Semifinals | Final | ||||||||
| 1 | Kokudo Ice Hockey Club | 3 | |||||||
| 4 | Nippon Paper Cranes | 2 | |||||||
| 1 | Kokudo Ice Hockey Club | 3 | |||||||
| 2 | Oji Seishi Hockey | 1 | |||||||
| 2 | Oji Seishi Hockey | 3 | |||||||
| 3 | Seibu Tetsudo | 0 | |||||||