| Competition: | Segunda División |
| Season: | 1998-99 |
| Winners: | Málaga CF |
| Promoted: | Málaga CF CD Numancia Sevilla CF Rayo Vallecano |
| Relegated: | RCD Mallorca B Barcelona B Hércules CF CD Orense |
| League Topscorer: |  Catanha |
| Matches: | 462 |
| Total Goals: | 1120 |
| Prevseason: | 1997-98 |
| Nextseason: | 1999-2000 |
The 1998–99 Segunda División season saw 22 teams participate in the second flight Spanish league. Málaga CF, CD Numancia, Sevilla FC and Rayo Vallecano were promoted to Primera División. RCD Mallorca B, Barcelona B, Hércules CF and CD Ourense were relegated to Segunda División B.
| Autonomous community | Number of teams | Teams | |
|---|---|---|---|
| 1 | 3 | Málaga, Recreativo, Sevilla | |
| 3 | Atlético Madrid B, Leganés, Rayo Vallecano | ||
| 3 | 2 | Albacete, Toledo | |
| 2 | Barcelona B, Lleida | ||
| 2 | Badajoz, Mérida | ||
| 2 | Compostela, Ourense | ||
| 7 | 1 | Sporting | |
| 1 | Mallorca B | ||
| 1 | Eibar | ||
| 1 | Las Palmas | ||
| 1 | Numancia | ||
| 1 | Logroñés | ||
| 1 | Osasuna | ||
| 1 | Hércules | ||
|}