| 1 | Sat 15 Sep 2012 | 2-1 v Bath CityBath City 1-2 Dover Athletic | Blue Square Bet South |
| 2 | Sat 29 Sep 2012 | 2-0 v Maidenhead UnitedDover Athletic 2-0 Maidenhead United | Blue Square Bet South |
| 3 | Tue 2 Oct 2012 | 1-1 v Welling UnitedWelling United 1-1 Dover Athletic | Blue Square Bet South |
| 4 | Sat 20 Oct 2012 | 1-3 v Salisbury CityDover Athletic 1-3 Salisbury City | Blue Square Bet South |
| 5 | Sat 27 Oct 2012 | 1-0 v Basingstoke TownBasingstoke Town 0-1 Dover Athletic | Blue Square Bet South |
| 6 | Sat 3 Nov 2012 | 3-0 v Eastbourne BoroughEastbourne Borough 0-3 Dover Athletic | Blue Square Bet South |
| 7 | Sat 17 Nov 2012 | 0-1 v Boreham WoodDover Athletic 0-1 Boreham Wood | Blue Square Bet South |
| 8 | Sat 24 Nov 2012 | 3-1 v Weston-super-MareDover Athletic 3-1 Weston-super-Mare | Blue Square Bet South |
| 9 | Sat 1 Dec 2012 | 2-1 v Billericay TownBillericay Town 1-2 Dover Athletic | Blue Square Bet South |
| 10 | Tue 1 Jan 2013 | 0-1 v Tonbridge AngelsDover Athletic 0-1 Tonbridge Angels | Blue Square Bet South |
| 11 | Sat 5 Jan 2013 | 0-1 v Staines TownDover Athletic 0-1 Staines Town | Blue Square Bet South |
| 12 | Sat 12 Jan 2013 | 2-5 v FarnboroughFarnborough 5-2 Dover Athletic | Blue Square Bet South |
| 13 | Tue 15 Jan 2013 | 0-1 v Dorchester TownDorchester Town 1-0 Dover Athletic | Blue Square Bet South |
| 14 | Sat 2 Feb 2013 | 3-2 v Truro CityDover Athletic 3-2 Truro City | Blue Square Bet South |
| 15 | Sat 9 Feb 2013 | 3-2 v Welling UnitedDover Athletic 3-2 Welling United | Blue Square Bet South |
| 16 | Sat 16 Feb 2013 | 3-0 v Weston-super-MareWeston-super-Mare 0-3 Dover Athletic | Blue Square Bet South |
| 17 | Sat 23 Feb 2013 | 1-1 v Boreham WoodBoreham Wood 1-1 Dover Athletic | Blue Square Bet South |
| 18 | Sat 2 Mar 2013 | 2-0 v Bath CityDover Athletic 2-0 Bath City | Blue Square Bet South |
| 19 | Tue 5 Mar 2013 | 2-1 v Maidenhead UnitedMaidenhead United 1-2 Dover Athletic | Blue Square Bet South |
| 20 | Sat 6 Apr 2013 | 0-5 v Basingstoke TownDover Athletic 0-5 Basingstoke Town | Blue Square Bet South |
| 21 | Tue 16 Apr 2013 | 1-1 v Havant & WaterloovilleHavant & Waterlooville 1-1 Dover Athletic | Blue Square Bet South |
| 22 | Sat 20 Apr 2013 | 0-0 v Dorchester TownDover Athletic 0-0 Dorchester Town | Blue Square Bet South |
| 23 | Tue 23 Apr 2013 | 2-0 v Staines TownStaines Town 0-2 Dover Athletic | Blue Square Bet South |
| 24 | Sat 27 Apr 2013 | 4-0 v BromleyBromley 0-4 Dover Athletic | Blue Square Bet South |
| 25 | Tue 30 Apr 2013 | 3-1 v EastleighEastleigh 1-3 Dover Athletic | Blue Square Bet South Play-off Semi Final |
| 26 | Sat 4 May 2013 | 0-2 v EastleighDover Athletic 0-2 Eastleigh | Blue Square Bet South Play-off Semi Final |
| 27 | Sun 12 May 2013 | 2-3 v Salisbury CitySalisbury City 3-2 Dover Athletic | Blue Square Bet South Play-off Final |
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