| 1. Round | 06/08/2016 | Cheltenham Town | - | Leyton Orient | 1:1 | ||||
| 2. Round | 13/08/2016 | Leyton Orient | - | Newport County | 0:1 | ||||
| 3. Round | 16/08/2016 | Leyton Orient | - | Stevenage FC | 3:0 | ||||
| 4. Round | 20/08/2016 | Grimsby Town | - | Leyton Orient | 1:2 | ||||
| 5. Round | 27/08/2016 | Leyton Orient | - | Mansfield Town | 1:2 | ||||
| 6. Round | 03/09/2016 | Morecambe FC | - | Leyton Orient | 1:2 |  |
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| 7. Round | 10/09/2016 | Carlisle United | - | Leyton Orient | 2:2 | ||||
| 8. Round | 17/09/2016 | Leyton Orient | - | Yeovil Town | 0:1 | ||||
| 9. Round | 24/09/2016 | Notts County | - | Leyton Orient | 3:1 | ||||
| 10. Round | 27/09/2016 | Leyton Orient | - | Plymouth Argyle | 0:2 | ||||
| 11. Round | 01/10/2016 | Barnet FC | - | Leyton Orient | 0:0 | ||||
| 14. Round | 22/10/2016 | Hartlepool United | - | Leyton Orient | 1:3 | ||||
| 15. Round | 29/10/2016 | Leyton Orient | - | Crewe Alexandra | 0:2 | ||||
| 20. Round | 10/12/2016 | Leyton Orient | - | Accrington Stanley | 1:0 | ||||
| 21. Round | 17/12/2016 | Wycombe Wanderers | - | Leyton Orient | 1:0 | ||||
| 22. Round | 26/12/2016 | Leyton Orient | - | Crawley Town | 3:2 | |
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| 26. Round | 14/01/2017 | Portsmouth FC | - | Leyton Orient | 2:1 |
England
