| 1 | Sat 6 Aug 2016 | 13-1 v Southend UnitedSouthend United 1-3 Gillingham | Sky Bet League One |
| 2 | Tue 9 Aug 2016 | 13-1 v Southend UnitedSouthend United 1-3 Gillingham | EFL Cup First Round |
| 3 | Sat 13 Aug 2016 | 12-1 v BuryGillingham 2-1 Bury | Sky Bet League One |
| 4 | Tue 16 Aug 2016 | 11-1 v Swindon TownGillingham 1-1 Swindon Town | Sky Bet League One |
| 5 | Sat 20 Aug 2016 | 10-5 v Scunthorpe UnitedScunthorpe United 5-0 Gillingham | Sky Bet League One |
| 6 | Tue 23 Aug 2016 | 12-1 v WatfordWatford 1-2 Gillingham | EFL Cup Second Round |
| 7 | Tue 30 Aug 2016 | 11-2 v Luton TownGillingham 1-2 Luton Town | Checkatrade Trophy Southern Group H |
| 8 | Wed 21 Sep 2016 | 10-5 v Tottenham HotspurTottenham Hotspur 5-0 Gillingham | EFL Cup Third Round |
| 9 | Sat 24 Sep 2016 | 12-1 v Coventry CityGillingham 2-1 Coventry City | Sky Bet League One |
| 10 | Tue 27 Sep 2016 | 13-3 v ChesterfieldChesterfield 3-3 Gillingham | Sky Bet League One |
| 11 | Sat 1 Oct 2016 | 10-2 v AFC WimbledonAFC Wimbledon 2-0 Gillingham | Sky Bet League One |
| 12 | Sat 8 Oct 2016 | 11-2 v Oldham AthleticGillingham 1-2 Oldham Athletic | Sky Bet League One |
| 13 | Sat 22 Oct 2016 | 11-1 v Charlton AthleticGillingham 1-1 Charlton Athletic | Sky Bet League One |
| 14 | Sat 29 Oct 2016 | 11-2 v Fleetwood TownFleetwood Town 2-1 Gillingham | Sky Bet League One |
| 15 | Sat 5 Nov 2016 | 12-2 v Brackley TownGillingham 2-2 Brackley Town | Emirates FA Cup First Round |
| 16 | Sat 12 Nov 2016 | 12-1 v Northampton TownGillingham 2-1 Northampton Town | Sky Bet League One |
| 17 | Wed 16 Nov 2016 | 13-4 v Brackley TownBrackley Town 4-3 Gillingham | Emirates FA Cup First Round |
| 18 | Sat 19 Nov 2016 | 12-1 v WalsallWalsall 1-2 Gillingham | Sky Bet League One |
| 19 | Tue 22 Nov 2016 | 10-1 v Oxford UnitedOxford United 1-0 Gillingham | Sky Bet League One |
| 20 | Sat 26 Nov 2016 | 13-0 v RochdaleGillingham 3-0 Rochdale | Sky Bet League One |
| 21 | Mon 12 Dec 2016 | 10-4 v Bolton WanderersBolton Wanderers 4-0 Gillingham | Sky Bet League One |
| 22 | Sat 17 Dec 2016 | 11-0 v Milton Keynes DonsGillingham 1-0 Milton Keynes Dons | Sky Bet League One |
| 23 | Mon 26 Dec 2016 | 11-1 v Peterborough UnitedPeterborough United 1-1 Gillingham | Sky Bet League One |
| 24 | Fri 30 Dec 2016 | 11-2 v MillwallMillwall 2-1 Gillingham | Sky Bet League One |
| 25 | Mon 2 Jan 2017 | 10-1 v Oxford UnitedGillingham 0-1 Oxford United | Sky Bet League One |
| 26 | Sat 14 Jan 2017 | 10-1 v Oldham AthleticOldham Athletic 1-0 Gillingham | Sky Bet League One |
| 27 | Sat 21 Jan 2017 | 12-2 v Sheffield UnitedSheffield United 2-2 Gillingham | Sky Bet League One |
| 28 | Sat 28 Jan 2017 | 11-1 v Shrewsbury TownGillingham 1-1 Shrewsbury Town | Sky Bet League One |
| 29 | Sat 4 Feb 2017 | 12-2 v Bradford CityBradford City 2-2 Gillingham | Sky Bet League One |
| 30 | Sat 11 Feb 2017 | 11-1 v Port ValeGillingham 1-1 Port Vale | Sky Bet League One |
| 31 | Tue 14 Feb 2017 | 11-1 v ChesterfieldGillingham 1-1 Chesterfield | Sky Bet League One |
| 32 | Sat 18 Feb 2017 | 11-2 v Coventry CityCoventry City 2-1 Gillingham | Sky Bet League One |
| 33 | Tue 21 Feb 2017 | 12-2 v AFC WimbledonGillingham 2-2 AFC Wimbledon | Sky Bet League One |
| 34 | Sat 25 Feb 2017 | 12-1 v Southend UnitedGillingham 2-1 Southend United | Sky Bet League One |
| 35 | Tue 28 Feb 2017 | 11-3 v Swindon TownSwindon Town 3-1 Gillingham | Sky Bet League One |
| 36 | Sat 4 Mar 2017 | 12-1 v BuryBury 1-2 Gillingham | Sky Bet League One |
| 37 | Sat 11 Mar 2017 | 13-2 v Scunthorpe UnitedGillingham 3-2 Scunthorpe United | Sky Bet League One |
| 38 | Tue 14 Mar 2017 | 10-4 v Bolton WanderersGillingham 0-4 Bolton Wanderers | Sky Bet League One |
| 39 | Sat 18 Mar 2017 | 11-4 v RochdaleRochdale 4-1 Gillingham | Sky Bet League One |
| 40 | Sun 30 Apr 2017 | 10-0 v Northampton TownNorthampton Town 0-0 Gillingham | Sky Bet League One |
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