| 1 | Sat 11 Aug 2012 | 45-4 v Nuneaton TownNuneaton Town 4-5 Ebbsfleet United | Blue Square Bet Premier |
| 2 | Tue 14 Aug 2012 | 40-1 v Braintree TownEbbsfleet United 0-1 Braintree Town | Blue Square Bet Premier |
| 3 | Sat 18 Aug 2012 | 41-1 v WrexhamEbbsfleet United 1-1 Wrexham | Blue Square Bet Premier |
| 4 | Sat 25 Aug 2012 | 42-4 v Hereford UnitedHereford United 4-2 Ebbsfleet United | Blue Square Bet Premier |
| 5 | Mon 27 Aug 2012 | 41-3 v Luton TownEbbsfleet United 1-3 Luton Town | Blue Square Bet Premier |
| 6 | Sat 1 Sep 2012 | 41-1 v Lincoln CityLincoln City 1-1 Ebbsfleet United | Blue Square Bet Premier |
| 7 | Tue 4 Sep 2012 | 41-4 v Forest Green RoversForest Green Rovers 4-1 Ebbsfleet United | Blue Square Bet Premier |
| 8 | Sat 8 Sep 2012 | 43-1 v Mansfield TownEbbsfleet United 3-1 Mansfield Town | Blue Square Bet Premier |
| 9 | Sat 15 Sep 2012 | 40-1 v SouthportSouthport 1-0 Ebbsfleet United | Blue Square Bet Premier |
| 10 | Tue 25 Sep 2012 | 42-2 v WokingEbbsfleet United 2-2 Woking | Blue Square Bet Premier |
| 11 | Sat 29 Sep 2012 | 41-3 v Stockport CountyStockport County 3-1 Ebbsfleet United | Blue Square Bet Premier |
| 12 | Sat 6 Oct 2012 | 41-1 v Kidderminster HarriersEbbsfleet United 1-1 Kidderminster Harriers | Blue Square Bet Premier |
| 13 | Sat 27 Oct 2012 | 41-0 v TamworthTamworth 0-1 Ebbsfleet United | Blue Square Bet Premier |
| 14 | Sat 3 Nov 2012 | 42-4 v Carlisle UnitedCarlisle United 4-2 Ebbsfleet United | FA Cup with Budweiser First Round |
| 15 | Tue 6 Nov 2012 | 42-2 v AFC Telford UnitedAFC Telford United 2-2 Ebbsfleet United | Blue Square Bet Premier |
| 16 | Sat 10 Nov 2012 | 43-2 v HydeEbbsfleet United 3-2 Hyde | Blue Square Bet Premier |
| 17 | Sat 1 Dec 2012 | 41-1 v Grimsby TownEbbsfleet United 1-1 Grimsby Town | Blue Square Bet Premier |
| 18 | Tue 4 Dec 2012 | 42-4 v Cambridge UnitedEbbsfleet United 2-4 Cambridge United | Blue Square Bet Premier |
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