| 4. Round | 20/08/2016 | Scunthorpe United | - | Gillingham FC | 5:0 | ||||
| 5. Round | 27/08/2016 | Shrewsbury Town | - | Gillingham FC | 2:3 | ||||
| 10. Round | 27/09/2016 | Chesterfield FC | - | Gillingham FC | 3:3 |  |
|||
| 11. Round | 01/10/2016 | AFC Wimbledon | - | Gillingham FC | 2:0 | ||||
| 25. Round | 02/01/2017 | Gillingham FC | - | Oxford United | 0:1 |
England