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| 1st(1st leg) | Elche CF | - | Benidorm CD | 1:1 | ||
| 2nd (2nd leg) | Benidorm CD | - | Elche CF | 2:1 | ||
| 1st(1st leg): 23/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: Benidorm CD | ||||
| 1st(1st leg) | UD Las Palmas | - | SD Compostela | 2:0 | ||
| 2nd (2nd leg) | SD Compostela | - | UD Las Palmas | 1:0 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: UD Las Palmas | ||||
| 1st(1st leg) | CD Tropezón | - | UE Lleida | 0:0 | ||
| 2nd (2nd leg) | UE Lleida | - | CD Tropezón | 4:0 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: UE Lleida | ||||
| 1st(1st leg) | CD Ourense | - | Sporting Gijón | 0:0 | ||
| 2nd (2nd leg) | Sporting Gijón | - | CD Ourense | 4:3 pso | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: Sporting Gijón | ||||
| 1st(1st leg) | CD Binéfar | - | CA Osasuna | 0:0 | ||
| 2nd (2nd leg) | CA Osasuna | - | CD Binéfar | 2:0 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: CA Osasuna | ||||
| 1st(1st leg) | UD SS Reyes | - | Albacete | 2:1 | ||
| 2nd (2nd leg) | Albacete | - | UD SS Reyes | 2:2 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: UD SS Reyes | ||||
| 1st(1st leg) | Cartagonova FC | - | Levante UD | 0:2 | ||
| 2nd (2nd leg) | Levante UD | - | Cartagonova FC | 4:1 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 06/10/1998 | Winner: Levante UD | ||||
| 1st(1st leg) | CP Cacereño | - | Sevilla FC | 0:4 | ||
| 2nd (2nd leg) | Sevilla FC | - | CP Cacereño | 2:2 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 06/10/1998 | Winner: Sevilla FC | ||||
| 1st(1st leg) | Jerez CF | - | Recreativo Huelva | 2:1 | ||
| 2nd (2nd leg) | Recreativo Huelva | - | Jerez CF | 0:1 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: Jerez CF | ||||
| 1st(1st leg) | Cádiz CF | - | Málaga CF | 1:3 | ||
| 2nd (2nd leg) | Málaga CF | - | Cádiz CF | 3:0 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: Málaga CF | ||||
| 1st(1st leg) | SD Beasain | - | CD Logroñés | 3:1 | ||
| 2nd (2nd leg) | CD Logroñés | - | SD Beasain | 0:0 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: SD Beasain | ||||
| 1st(1st leg) | Barakaldo CF | - | CD Numancia | 0:2 | ||
| 2nd (2nd leg) | CD Numancia | - | Barakaldo CF | 3:2 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: CD Numancia | ||||
| 1st(1st leg) | Talavera CF | - | CD Leganés | 0:0 | ||
| 2nd (2nd leg) | CD Leganés | - | Talavera CF | 1:1 | ||
| 1st(1st leg): 24/09/1998 | 2nd (2nd leg): 07/10/1998 | Winner: Talavera CF | ||||
| 1st(1st leg) | AD Ceuta | - | CD Badajoz | 0:1 | ||
| 2nd (2nd leg) | CD Badajoz | - | AD Ceuta | 2:1 | ||
| 1st(1st leg): 01/10/1998 | 2nd (2nd leg): 07/10/1998 | Winner: CD Badajoz | ||||
