| 1 | Sat 29 Sep 2012 | 161-3 v Stockport CountyStockport County 3-1 Ebbsfleet United | Blue Square Bet Premier |
| 2 | Sat 6 Oct 2012 | 161-1 v Kidderminster HarriersEbbsfleet United 1-1 Kidderminster Harriers | Blue Square Bet Premier |
| 3 | Sat 3 Nov 2012 | 162-4 v Carlisle UnitedCarlisle United 4-2 Ebbsfleet United | FA Cup with Budweiser First Round |
| 4 | Sat 17 Nov 2012 | 162-1 v Macclesfield TownMacclesfield Town 1-2 Ebbsfleet United | Blue Square Bet Premier |
| 5 | Sat 1 Dec 2012 | 161-1 v Grimsby TownEbbsfleet United 1-1 Grimsby Town | Blue Square Bet Premier |
| 6 | Tue 4 Dec 2012 | 162-4 v Cambridge UnitedEbbsfleet United 2-4 Cambridge United | Blue Square Bet Premier |
| 7 | Sat 8 Dec 2012 | 161-4 v Mansfield TownMansfield Town 4-1 Ebbsfleet United | Blue Square Bet Premier |
| 8 | Wed 26 Dec 2012 | 161-3 v DartfordDartford 3-1 Ebbsfleet United | Blue Square Bet Premier |
| 9 | Sat 5 Jan 2013 | 161-1 v Lincoln CityEbbsfleet United 1-1 Lincoln City | Blue Square Bet Premier |
| 10 | Sun 13 Jan 2013 | 160-1 v WokingWoking 1-0 Ebbsfleet United | Blue Square Bet Premier |
| 11 | Sat 9 Feb 2013 | 163-1 v GatesheadEbbsfleet United 3-1 Gateshead | Blue Square Bet Premier |
| 12 | Sat 16 Feb 2013 | 160-0 v Stockport CountyEbbsfleet United 0-0 Stockport County | Blue Square Bet Premier |
| 13 | Tue 19 Feb 2013 | 161-0 v Hereford UnitedEbbsfleet United 1-0 Hereford United | Blue Square Bet Premier |
| 14 | Tue 26 Feb 2013 | 161-3 v Grimsby TownGrimsby Town 3-1 Ebbsfleet United | Blue Square Bet Premier |
| 15 | Sat 2 Mar 2013 | 162-3 v Kidderminster HarriersKidderminster Harriers 3-2 Ebbsfleet United | Blue Square Bet Premier |
| 16 | Tue 5 Mar 2013 | 161-4 v WrexhamWrexham 4-1 Ebbsfleet United | Blue Square Bet Premier |
| 17 | Sat 9 Mar 2013 | 161-1 v Newport CountyEbbsfleet United 1-1 Newport County | Blue Square Bet Premier |
| 18 | Tue 12 Mar 2013 | 160-3 v Alfreton TownAlfreton Town 3-0 Ebbsfleet United | Blue Square Bet Premier |
| 19 | Sat 16 Mar 2013 | 164-1 v SouthportEbbsfleet United 4-1 Southport | Blue Square Bet Premier |
| 20 | Tue 19 Mar 2013 | 161-1 v Cambridge UnitedCambridge United 1-1 Ebbsfleet United | Blue Square Bet Premier |
| 21 | Sat 30 Mar 2013 | 160-2 v Forest Green RoversEbbsfleet United 0-2 Forest Green Rovers | Blue Square Bet Premier |
| 22 | Mon 1 Apr 2013 | 161-3 v Braintree TownBraintree Town 3-1 Ebbsfleet United | Blue Square Bet Premier |
| 23 | Wed 3 Apr 2013 | 161-1 v BarrowBarrow 1-1 Ebbsfleet United | Blue Square Bet Premier |
| 24 | Sat 6 Apr 2013 | 161-1 v Nuneaton TownEbbsfleet United 1-1 Nuneaton Town | Blue Square Bet Premier |
| 25 | Tue 9 Apr 2013 | 160-1 v HydeHyde 1-0 Ebbsfleet United | Blue Square Bet Premier |
| 26 | Sat 13 Apr 2013 | 161-3 v AFC Telford UnitedEbbsfleet United 1-3 AFC Telford United | Blue Square Bet Premier |
| 27 | Tue 16 Apr 2013 | 161-1 v TamworthEbbsfleet United 1-1 Tamworth | Blue Square Bet Premier |
| 28 | Thu 18 Apr 2013 | 160-2 v Luton TownLuton Town 2-0 Ebbsfleet United | Blue Square Bet Premier |
| 29 | Sat 20 Apr 2013 | 160-2 v GatesheadGateshead 2-0 Ebbsfleet United | Blue Square Bet Premier |
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