The 1988-89 Segunda División season saw 20 teams participate in the second flight Spanish league. CD Castellón, Rayo Vallecano, CD Tenerife and RCD Mallorca were promoted to Primera División. Barcelona Atlètic, UD Alzira, UE Lleida and CFJ Mollerussa were relegated to Segunda División B.
| Key to colors in league table: |
| Promoted to Primera División |
| Promotion playoff |
| Relegated to Segunda División B |
| Position | Club | Played | Points | Wins | Draws | Losses | Goals for | Goals against | Goal Difference |
|---|---|---|---|---|---|---|---|---|---|
| 1 | CD Castellón | 38 | 51+13 | 21 | 9 | 8 | 49 | 29 | +20 |
| 2 | Rayo Vallecano | 38 | 49+11 | 19 | 11 | 8 | 61 | 36 | +25 |
| 3 | CD Tenerife | 38 | 48+10 | 20 | 8 | 10 | 54 | 36 | +18 |
| 4 | RCD Mallorca | 38 | 48+10 | 21 | 6 | 11 | 51 | 26 | +25 |
| 5 | Recreativo de Huelva | 38 | 42+4 | 16 | 10 | 12 | 46 | 36 | +10 |
| 6 | Racing de Santander | 38 | 42+4 | 17 | 8 | 13 | 56 | 43 | +13 |
| 7 | UD Salamanca | 38 | 42+4 | 14 | 14 | 10 | 35 | 33 | +2 |
| 8 | Sestao | 38 | 41+3 | 14 | 13 | 11 | 39 | 32 | +7 |
| 9 | UE Figueres | 38 | 41+3 | 16 | 9 | 13 | 52 | 50 | +2 |
| 10 | Deportivo de La Coruña | 38 | 40+2 | 16 | 8 | 14 | 43 | 35 | +8 |
| 11 | UD Las Palmas | 38 | 40+2 | 15 | 10 | 13 | 52 | 53 | -1 |
| 12 | Xerez CD | 38 | 40+2 | 13 | 14 | 11 | 40 | 38 | +2 |
| 13 | CE Sabadell FC | 38 | 39+1 | 15 | 9 | 14 | 49 | 43 | +6 |
| 14 | Real Burgos | 38 | 36-2 | 9 | 18 | 11 | 27 | 34 | -7 |
| 15 | Castilla CF | 38 | 36-2 | 13 | 10 | 15 | 50 | 59 | -9 |
| 16 | SD Eibar | 38 | 34-4 | 8 | 18 | 12 | 36 | 42 | -6 |
| 17 | Barcelona Atlètic | 38 | 28-10 | 8 | 12 | 18 | 42 | 58 | -16 |
| 18 | UD Alzira | 38 | 26-12 | 9 | 8 | 21 | 29 | 58 | -29 |
| 19 | UE Lleida | 38 | 26-12 | 8 | 10 | 20 | 29 | 43 | -16 |
| 20 | CFJ Mollerussa | 38 | 11-27 | 3 | 5 | 30 | 19 | 75 | -56 |
| Home Matches: | |||
| RCD Español | 1-0 | RCD Mallorca | |
| CD Tenerife | 4-0 | Real Betis |
| Away Matches: | |||
| RCD Mallorca | 2-0 | RCD Español | Agg:2-1 |
| Real Betis | 1-0 | CD Tenerife | Agg:1-4 |
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