| 2. Round | 22/08/2016 | West Bromwich Albion U23 | - | Fulham FC U23 | 2:1 | ||||
| 3. Round | 26/08/2016 | Brighton & Hove Albion U23 | - | Fulham FC U23 | 1:0 | ||||
| 4. Round | 12/09/2016 | Fulham FC U23 | - | Aston Villa U23 | 3:0 | ||||
| 5. Round | 17/09/2016 | Stoke City U23 | - | Fulham FC U23 | 1:2 | ||||
| 6. Round | 26/09/2016 | Fulham FC U23 | - | Norwich City U23 | 0:1 | ||||
| 7. Round | 17/10/2016 | Swansea City U23 | - | Fulham FC U23 | 2:0 | ||||
| 14. Round | 07/01/2017 | Fulham FC U23 | - | Stoke City U23 | 2:0 | ||||
| 15. Round | 16/01/2017 | Norwich City U23 | - | Fulham FC U23 | 2:2 | ||||
| 16. Round | 30/01/2017 | Fulham FC U23 | - | Swansea City U23 | 2:1 | ||||
| 17. Round | 06/02/2017 | Fulham FC U23 | - | Middlesbrough FC U23 | 1:0 |  |
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| 18. Round | 20/02/2017 | West Ham United U23 | - | Fulham FC U23 | 2:0 | ||||
| 19. Round | 18/04/2017 | Blackburn Rovers U23 | - | Fulham FC U23 | 3:2 | ||||
| 22. Round | 24/04/2017 | Fulham FC U23 | - | Wolverhampton Wanderers U23 | 1:4 |
Estonia