| 2. Round | 27/08/2016 | FC Jumilla | - | Extremadura UD | 2:0 |  |
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| 5. Round | 18/09/2016 | Extremadura UD | - | Linares Deportivo | 1:2 | ||||
| 6. Round | 25/09/2016 | Córdoba CF B | - | Extremadura UD | 0:0 | ||||
| 12. Round | 02/11/2016 | UD Melilla | - | Extremadura UD | 0:1 | ||||
| 13. Round | 06/11/2016 | Extremadura UD | - | Granada CF B | 1:1 | ||||
| 14. Round | 13/11/2016 | San Fernando CD | - | Extremadura UD | 1:3 | ||||
| 16. Round | 27/11/2016 | Marbella FC | - | Extremadura UD | 3:2 | ||||
| 17. Round | 04/12/2016 | Extremadura UD | - | Real Jaén | 1:1 | ||||
| 18. Round | 11/12/2016 | Atlético Sanluqueño CF | - | Extremadura UD | 3:0 | |
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| 19. Round | 18/12/2016 | Extremadura UD | - | Real Murcia | 0:2 | ||||
| 20. Round | 08/01/2017 | CF Villanovense | - | Extremadura UD | 0:0 | ||||
| 22. Round | 22/01/2017 | RB Linense | - | Extremadura UD | 1:0 |
Spain