1. Round | 06/08/2016 | Southend United | - | Gillingham FC | 1:3 | ||||
2. Round | 13/08/2016 | Gillingham FC | - | Bury FC | 2:1 | ||||
3. Round | 16/08/2016 | Gillingham FC | - | Swindon Town | 1:1 | ||||
4. Round | 20/08/2016 | Scunthorpe United | - | Gillingham FC | 5:0 | ||||
5. Round | 27/08/2016 | Shrewsbury Town | - | Gillingham FC | 2:3 | ||||
6. Round | 04/09/2016 | Gillingham FC | - | Sheffield United | 1:2 | ||||
9. Round | 24/09/2016 | Gillingham FC | - | Coventry City | 2:1 | ||||
10. Round | 27/09/2016 | Chesterfield FC | - | Gillingham FC | 3:3 | ||||
11. Round | 01/10/2016 | AFC Wimbledon | - | Gillingham FC | 2:0 | ||||
14. Round | 18/10/2016 | Gillingham FC | - | Walsall FC | 1:1 | ||||
15. Round | 22/10/2016 | Gillingham FC | - | Charlton Athletic | 1:1 | ||||
16. Round | 29/10/2016 | Fleetwood Town | - | Gillingham FC | 2:1 | ||||
17. Round | 12/11/2016 | Gillingham FC | - | Northampton Town | 2:1 | ||||
18. Round | 19/11/2016 | Walsall FC | - | Gillingham FC | 1:2 | ||||
19. Round | 22/11/2016 | Oxford United | - | Gillingham FC | 1:0 | ||||
20. Round | 26/11/2016 | Gillingham FC | - | Rochdale AFC | 3:0 | ||||
27. Round | 14/01/2017 | Oldham Athletic | - | Gillingham FC | 1:0 |