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| 1st(1st leg) | UE Lleida | - | Águilas CF | 3:0 | ||
| 2nd (2nd leg) | Águilas CF | - | UE Lleida | 1:1 | ||
| 1st(1st leg): 01/09/1998 | 2nd (2nd leg): 08/09/1998 | Winner: UE Lleida | ||||
| 1st(1st leg) | CD Leonesa | - | CD Numancia | 2:2 | ||
| 2nd (2nd leg) | CD Numancia | - | CD Leonesa | 1:1 | ||
| 1st(1st leg): 01/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: CD Numancia | ||||
| 1st(1st leg) | Algeciras CF | - | Recreativo Huelva | 1:0 | ||
| 2nd (2nd leg) | Recreativo Huelva | - | Algeciras CF | 3:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Recreativo Huelva | ||||
| 1st(1st leg) | Real Jaén | - | Sevilla FC | 1:1 | ||
| 2nd (2nd leg) | Sevilla FC | - | Real Jaén | 2:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Sevilla FC | ||||
| 1st(1st leg) | Universidad Las Palmas | - | SD Compostela | 1:1 | ||
| 2nd (2nd leg) | SD Compostela | - | Universidad Las Palmas | 2:1 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: SD Compostela | ||||
| 1st(1st leg) | CD Lalín | - | UD Las Palmas | 1:0 | ||
| 2nd (2nd leg) | UD Las Palmas | - | CD Lalín | 4:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: UD Las Palmas | ||||
| 1st(1st leg) | Jerez CF | - | Rayo Vallecano | 2:2 | ||
| 2nd (2nd leg) | Rayo Vallecano | - | Jerez CF | 1:2 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 08/09/1998 | Winner: Jerez CF | ||||
| 1st(1st leg) | UD SS Reyes | - | CP Mérida | 1:0 | ||
| 2nd (2nd leg) | CP Mérida | - | UD SS Reyes | 2:1 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: UD SS Reyes | ||||
| 1st(1st leg) | Elche CF | - | Hércules CF | 1:0 | ||
| 2nd (2nd leg) | Hércules CF | - | Elche CF | 1:1 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Elche CF | ||||
| 1st(1st leg) | Terrassa FC | - | Levante UD | 1:1 | ||
| 2nd (2nd leg) | Levante UD | - | Terrassa FC | 3:1 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Levante UD | ||||
| 1st(1st leg) | CD Lealtad | - | Sporting Gijón | 2:1 | ||
| 2nd (2nd leg) | Sporting Gijón | - | CD Lealtad | 3:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Sporting Gijón | ||||
| 1st(1st leg) | SD Noja | - | CA Osasuna | 0:1 | ||
| 2nd (2nd leg) | CA Osasuna | - | SD Noja | 3:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: CA Osasuna | ||||
| 1st(1st leg) | SD Beasain | - | SD Eibar | 0:0 | ||
| 2nd (2nd leg) | SD Eibar | - | SD Beasain | 1:1 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: SD Beasain | ||||
| 1st(1st leg) | CD Móstoles | - | CD Badajoz | 1:2 | ||
| 2nd (2nd leg) | CD Badajoz | - | CD Móstoles | 2:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: CD Badajoz | ||||
| 1st(1st leg) | Cádiz CF | - | Granada CF | 2:2 | ||
| 2nd (2nd leg) | Granada CF | - | Cádiz CF | 1:2 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Cádiz CF | ||||
| 1st(1st leg) | Xerez CD | - | Málaga CF | 2:1 | ||
| 2nd (2nd leg) | Málaga CF | - | Xerez CD | 2:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Málaga CF | ||||
| 1st(1st leg) | UB Conquense | - | Albacete | 0:3 | ||
| 2nd (2nd leg) | Albacete | - | UB Conquense | 1:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Albacete | ||||
| 1st(1st leg) | Talavera CF | - | CD Toledo | 1:1 | ||
| 2nd (2nd leg) | CD Toledo | - | Talavera CF | 0:2 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Talavera CF | ||||
| 1st(1st leg) | CD Calahorra | - | CD Ourense | 1:1 | ||
| 2nd (2nd leg) | CD Ourense | - | CD Calahorra | 2:0 | ||
| 1st(1st leg): 02/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: CD Ourense | ||||
| 1st(1st leg) | Palamós CF | - | Benidorm CD | 1:1 | ||
| 2nd (2nd leg) | Benidorm CD | - | Palamós CF | 3:1 | ||
| 1st(1st leg): 03/09/1998 | 2nd (2nd leg): 09/09/1998 | Winner: Benidorm CD | ||||
