| 4. Round | 12/09/2016 | Middlesbrough FC U23 | - | Swansea City U23 | 2:1 | ||||
| 5. Round | 19/09/2016 | Wolverhampton Wanderers U23 | - | Middlesbrough FC U23 | 2:1 | ||||
| 6. Round | 26/09/2016 | Middlesbrough FC U23 | - | Aston Villa U23 | 1:2 |  |
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| 9. Round | 31/10/2016 | Newcastle United U23 | - | Middlesbrough FC U23 | 2:0 | ||||
| 10. Round | 18/11/2016 | Middlesbrough FC U23 | - | Fulham FC U23 | 1:4 | |
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| 12. Round | 12/12/2016 | Middlesbrough FC U23 | - | Norwich City U23 | 2:2 | |
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| 13. Round | 19/12/2016 | Swansea City U23 | - | Middlesbrough FC U23 | 3:2 | ||||
| 15. Round | 16/01/2017 | Aston Villa U23 | - | Middlesbrough FC U23 | 0:0 | ||||
| 18. Round | 20/02/2017 | Middlesbrough FC U23 | - | West Bromwich Albion U23 | 2:1 | |
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| 19. Round | 03/03/2017 | Brighton & Hove Albion U23 | - | Middlesbrough FC U23 | 4:2 | |
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| 20. Round | 13/03/2017 | Middlesbrough FC U23 | - | Blackburn Rovers U23 | 4:1 | ||||
| 21. Round | 10/04/2017 | West Ham United U23 | - | Middlesbrough FC U23 | 1:3 | ||||
| 14. Round | 17/04/2017 | Middlesbrough FC U23 | - | Wolverhampton Wanderers U23 | 0:1 | ||||
| 22. Round | 21/04/2017 | Middlesbrough FC U23 | - | Newcastle United U23 | 0:2 | |
England