| 1 | Sat 11 Aug 2012 | 21-1 v Grimsby TownSouthport 1-1 Grimsby Town | Blue Square Bet Premier |
| 2 | Tue 14 Aug 2012 | 23-3 v Alfreton TownAlfreton Town 3-3 Southport | Blue Square Bet Premier |
| 3 | Sat 18 Aug 2012 | 20-2 v Cambridge UnitedCambridge United 2-0 Southport | Blue Square Bet Premier |
| 4 | Sat 25 Aug 2012 | 20-3 v TamworthSouthport 0-3 Tamworth | Blue Square Bet Premier |
| 5 | Mon 27 Aug 2012 | 22-0 v HydeHyde 0-2 Southport | Blue Square Bet Premier |
| 6 | Sat 1 Sep 2012 | 20-3 v AFC Telford UnitedSouthport 0-3 AFC Telford United | Blue Square Bet Premier |
| 7 | Tue 4 Sep 2012 | 22-1 v GatesheadSouthport 2-1 Gateshead | Blue Square Bet Premier |
| 8 | Sat 8 Sep 2012 | 22-2 v Kidderminster HarriersKidderminster Harriers 2-2 Southport | Blue Square Bet Premier |
| 9 | Sat 15 Sep 2012 | 21-0 v Ebbsfleet UnitedSouthport 1-0 Ebbsfleet United | Blue Square Bet Premier |
| 10 | Sat 22 Sep 2012 | 21-2 v Newport CountyNewport County 2-1 Southport | Blue Square Bet Premier |
| 11 | Tue 25 Sep 2012 | 21-1 v Stockport CountySouthport 1-1 Stockport County | Blue Square Bet Premier |
| 12 | Sat 29 Sep 2012 | 21-3 v Luton TownLuton Town 3-1 Southport | Blue Square Bet Premier |
| 13 | Tue 9 Oct 2012 | 22-3 v BarrowBarrow 3-2 Southport | Blue Square Bet Premier |
| 14 | Sat 27 Oct 2012 | 22-2 v Hereford UnitedSouthport 2-2 Hereford United | Blue Square Bet Premier |
| 15 | Tue 6 Nov 2012 | 21-4 v WrexhamSouthport 1-4 Wrexham | Blue Square Bet Premier |
| 16 | Sat 10 Nov 2012 | 20-1 v Mansfield TownMansfield Town 1-0 Southport | Blue Square Bet Premier |
| 17 | Sat 17 Nov 2012 | 22-2 v DartfordDartford 2-2 Southport | Blue Square Bet Premier |
| 18 | Sat 1 Dec 2012 | 24-3 v Stockport CountyStockport County 3-4 Southport | Blue Square Bet Premier |
| 19 | Sat 8 Dec 2012 | 20-2 v Braintree TownSouthport 0-2 Braintree Town | Blue Square Bet Premier |
| 20 | Wed 26 Dec 2012 | 23-2 v Macclesfield TownSouthport 3-2 Macclesfield Town | Blue Square Bet Premier |
| 21 | Sat 29 Dec 2012 | 20-1 v HydeSouthport 0-1 Hyde | Blue Square Bet Premier |
| 22 | Tue 1 Jan 2013 | 22-2 v Macclesfield TownMacclesfield Town 2-2 Southport | Blue Square Bet Premier |
| 23 | Sat 5 Jan 2013 | 23-1 v AFC Telford UnitedAFC Telford United 1-3 Southport | Blue Square Bet Premier |
| 24 | Tue 8 Jan 2013 | 24-2 v Lincoln CitySouthport 4-2 Lincoln City | Blue Square Bet Premier |
| 25 | Sat 19 Jan 2013 | 21-2 v Mansfield TownSouthport 1-2 Mansfield Town | Blue Square Bet Premier |
| 26 | Tue 29 Jan 2013 | 22-2 v WrexhamWrexham 2-2 Southport | Blue Square Bet Premier |
| 27 | Sat 2 Feb 2013 | 22-2 v Hereford UnitedHereford United 2-2 Southport | Blue Square Bet Premier |
| 28 | Sat 9 Feb 2013 | 21-0 v Nuneaton TownNuneaton Town 0-1 Southport | Blue Square Bet Premier |
| 29 | Tue 12 Feb 2013 | 25-2 v BarrowSouthport 5-2 Barrow | Blue Square Bet Premier |
| 30 | Sat 23 Feb 2013 | 21-2 v WokingSouthport 1-2 Woking | Blue Square Bet Premier |
| 31 | Sat 2 Mar 2013 | 22-2 v DartfordSouthport 2-2 Dartford | Blue Square Bet Premier |
| 32 | Tue 5 Mar 2013 | 22-1 v Cambridge UnitedSouthport 2-1 Cambridge United | Blue Square Bet Premier |
| 33 | Sat 9 Mar 2013 | 20-1 v Lincoln CityLincoln City 1-0 Southport | Blue Square Bet Premier |
| 34 | Tue 12 Mar 2013 | 21-2 v Forest Green RoversSouthport 1-2 Forest Green Rovers | Blue Square Bet Premier |
| 35 | Sat 16 Mar 2013 | 21-4 v Ebbsfleet UnitedEbbsfleet United 4-1 Southport | Blue Square Bet Premier |
| 36 | Tue 19 Mar 2013 | 21-2 v TamworthTamworth 2-1 Southport | Blue Square Bet Premier |
| 37 | Tue 26 Mar 2013 | 20-2 v Newport CountySouthport 0-2 Newport County | Blue Square Bet Premier |
| 38 | Sat 30 Mar 2013 | 22-2 v GatesheadGateshead 2-2 Southport | Blue Square Bet Premier |
| 39 | Mon 1 Apr 2013 | 20-2 v Alfreton TownSouthport 0-2 Alfreton Town | Blue Square Bet Premier |
| 40 | Wed 3 Apr 2013 | 23-1 v Braintree TownBraintree Town 1-3 Southport | Blue Square Bet Premier |
| 41 | Sat 6 Apr 2013 | 22-2 v Grimsby TownGrimsby Town 2-2 Southport | Blue Square Bet Premier |
| 42 | Sat 13 Apr 2013 | 21-0 v Forest Green RoversForest Green Rovers 0-1 Southport | Blue Square Bet Premier |
| 43 | Sat 20 Apr 2013 | 21-3 v Luton TownSouthport 1-3 Luton Town | Blue Square Bet Premier |
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