| 1 | Tue 14 Aug 2012 | 22-1 v Bristol CityBristol City 1-2 Gillingham | Capital One Cup First Round |
| 2 | Sat 18 Aug 2012 | 23-1 v Bradford CityGillingham 3-1 Bradford City | npower League Two |
| 3 | Tue 21 Aug 2012 | 21-0 v Wycombe WanderersWycombe Wanderers 0-1 Gillingham | npower League Two |
| 4 | Sat 25 Aug 2012 | 22-1 v Dagenham & RedbridgeDagenham & Redbridge 1-2 Gillingham | npower League Two |
| 5 | Tue 28 Aug 2012 | 20-2 v MiddlesbroughGillingham 0-2 Middlesbrough | Capital One Cup Second Round |
| 6 | Sat 1 Sep 2012 | 21-1 v ChesterfieldGillingham 1-1 Chesterfield | npower League Two |
| 7 | Tue 4 Sep 2012 | 22-3 v Crawley TownCrawley Town 3-2 Gillingham | Johnstone's Paint Trophy First Round |
| 8 | Sat 8 Sep 2012 | 23-1 v BarnetBarnet 1-3 Gillingham | npower League Two |
| 9 | Sat 15 Sep 2012 | 24-0 v Bristol RoversGillingham 4-0 Bristol Rovers | npower League Two |
| 10 | Tue 18 Sep 2012 | 21-0 v Southend UnitedGillingham 1-0 Southend United | npower League Two |
| 11 | Sat 22 Sep 2012 | 22-0 v Port ValePort Vale 0-2 Gillingham | npower League Two |
| 12 | Sat 29 Sep 2012 | 21-2 v RochdaleGillingham 1-2 Rochdale | npower League Two |
| 13 | Tue 2 Oct 2012 | 22-1 v Northampton TownNorthampton Town 1-2 Gillingham | npower League Two |
| 14 | Sat 6 Oct 2012 | 20-0 v Oxford UnitedOxford United 0-0 Gillingham | npower League Two |
| 15 | Sat 20 Oct 2012 | 24-1 v Burton AlbionGillingham 4-1 Burton Albion | npower League Two |
| 16 | Tue 23 Oct 2012 | 21-2 v Torquay UnitedTorquay United 2-1 Gillingham | npower League Two |
| 17 | Sat 27 Oct 2012 | 21-0 v AFC WimbledonAFC Wimbledon 0-1 Gillingham | npower League Two |
| 18 | Sat 3 Nov 2012 | 24-0 v Scunthorpe UnitedGillingham 4-0 Scunthorpe United | FA Cup with Budweiser First Round |
| 19 | Tue 6 Nov 2012 | 20-0 v Cheltenham TownGillingham 0-0 Cheltenham Town | npower League Two |
| 20 | Sat 10 Nov 2012 | 22-2 v Plymouth ArgylePlymouth Argyle 2-2 Gillingham | npower League Two |
| 21 | Sat 17 Nov 2012 | 22-1 v MorecambeGillingham 2-1 Morecambe | npower League Two |
| 22 | Tue 20 Nov 2012 | 22-3 v Exeter CityGillingham 2-3 Exeter City | npower League Two |
| 23 | Sat 24 Nov 2012 | 21-1 v Accrington StanleyAccrington Stanley 1-1 Gillingham | npower League Two |
| 24 | Sat 1 Dec 2012 | 20-2 v Preston North EndPreston North End 2-0 Gillingham | FA Cup with Budweiser Second Round |
| 25 | Sat 8 Dec 2012 | 22-1 v Rotherham UnitedRotherham United 1-2 Gillingham | npower League Two |
| 26 | Sat 15 Dec 2012 | 22-2 v Fleetwood TownGillingham 2-2 Fleetwood Town | npower League Two |
| 27 | Wed 26 Dec 2012 | 20-1 v BarnetGillingham 0-1 Barnet | npower League Two |
| 28 | Tue 1 Jan 2013 | 21-0 v Southend UnitedSouthend United 0-1 Gillingham | npower League Two |
| 29 | Sat 5 Jan 2013 | 22-0 v Bristol RoversBristol Rovers 0-2 Gillingham | npower League Two |
| 30 | Sat 12 Jan 2013 | 21-2 v Port ValeGillingham 1-2 Port Vale | npower League Two |
| 31 | Sat 26 Jan 2013 | 21-1 v York CityGillingham 1-1 York City | npower League Two |
| 32 | Tue 29 Jan 2013 | 22-0 v Northampton TownGillingham 2-0 Northampton Town | npower League Two |
| 33 | Mon 4 Feb 2013 | 20-1 v Wycombe WanderersGillingham 0-1 Wycombe Wanderers | npower League Two |
| 34 | Sat 9 Feb 2013 | 21-0 v Bradford CityBradford City 0-1 Gillingham | npower League Two |
| 35 | Tue 12 Feb 2013 | 20-0 v York CityYork City 0-0 Gillingham | npower League Two |
| 36 | Sat 16 Feb 2013 | 22-1 v Dagenham & RedbridgeGillingham 2-1 Dagenham & Redbridge | npower League Two |
| 37 | Sat 23 Feb 2013 | 21-0 v ChesterfieldChesterfield 0-1 Gillingham | npower League Two |
| 38 | Sat 2 Mar 2013 | 21-1 v Aldershot TownAldershot Town 1-1 Gillingham | npower League Two |
| 39 | Sat 9 Mar 2013 | 22-1 v Plymouth ArgyleGillingham 2-1 Plymouth Argyle | npower League Two |
| 40 | Tue 12 Mar 2013 | 20-0 v Exeter CityExeter City 0-0 Gillingham | npower League Two |
| 41 | Sat 16 Mar 2013 | 21-1 v MorecambeMorecambe 1-1 Gillingham | npower League Two |
| 42 | Tue 19 Mar 2013 | 21-1 v RochdaleRochdale 1-1 Gillingham | npower League Two |
| 43 | Sat 23 Mar 2013 | 21-0 v Accrington StanleyGillingham 1-0 Accrington Stanley | npower League Two |
| 44 | Sat 30 Mar 2013 | 22-2 v Fleetwood TownFleetwood Town 2-2 Gillingham | npower League Two |
| 45 | Mon 1 Apr 2013 | 21-0 v Rotherham UnitedGillingham 1-0 Rotherham United | npower League Two |
| 46 | Sat 6 Apr 2013 | 21-0 v Torquay UnitedGillingham 1-0 Torquay United | npower League Two |
| 47 | Sat 13 Apr 2013 | 20-1 v Cheltenham TownCheltenham Town 1-0 Gillingham | npower League Two |
| 48 | Sat 20 Apr 2013 | 22-2 v AFC WimbledonGillingham 2-2 AFC Wimbledon | npower League Two |
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