| 1 | Tue 14 Aug 2012 | 30-4 v Peterborough UnitedPeterborough United 4-0 Southend United | Capital One Cup First Round |
| 2 | Tue 21 Aug 2012 | 30-2 v Oxford UnitedOxford United 2-0 Southend United | npower League Two |
| 3 | Sat 1 Sep 2012 | 31-0 v Wycombe WanderersSouthend United 1-0 Wycombe Wanderers | npower League Two |
| 4 | Tue 4 Sep 2012 | 32-1 v AFC WimbledonSouthend United 2-1 AFC Wimbledon | Johnstone's Paint Trophy First Round |
| 5 | Sat 8 Sep 2012 | 33-1 v Dagenham & RedbridgeSouthend United 3-1 Dagenham & Redbridge | npower League Two |
| 6 | Sat 15 Sep 2012 | 33-1 v Cheltenham TownCheltenham Town 1-3 Southend United | npower League Two |
| 7 | Tue 18 Sep 2012 | 30-1 v GillinghamGillingham 1-0 Southend United | npower League Two |
| 8 | Sat 6 Oct 2012 | 32-2 v BarnetSouthend United 2-2 Barnet | npower League Two |
| 9 | Sat 20 Oct 2012 | 30-1 v MorecambeMorecambe 1-0 Southend United | npower League Two |
| 10 | Tue 23 Oct 2012 | 31-2 v Aldershot TownSouthend United 1-2 Aldershot Town | npower League Two |
| 11 | Sat 27 Oct 2012 | 30-0 v York CitySouthend United 0-0 York City | npower League Two |
| 12 | Tue 4 Dec 2012 | 32-1 v BrentfordSouthend United 2-1 Brentford | Johnstone's Paint Trophy Southern Area Quarter Final |
| 13 | Sat 8 Dec 2012 | 30-0 v Fleetwood TownFleetwood Town 0-0 Southend United | npower League Two |
| 14 | Fri 21 Dec 2012 | 33-0 v ChesterfieldSouthend United 3-0 Chesterfield | npower League Two |
| 15 | Tue 8 Jan 2013 | 33-3 v Oxford UnitedOxford United 3-3 Southend United | Johnstone's Paint Trophy Southern Area Semi Final |
| 16 | Tue 15 Jan 2013 | 31-2 v BrentfordBrentford 2-1 Southend United | FA Cup with Budweiser Third Round Replay |
| 17 | Sat 9 Feb 2013 | 31-1 v Accrington StanleyAccrington Stanley 1-1 Southend United | npower League Two |
| 18 | Tue 12 Feb 2013 | 31-2 v Cheltenham TownSouthend United 1-2 Cheltenham Town | npower League Two |
| 19 | Sat 16 Feb 2013 | 31-2 v Northampton TownSouthend United 1-2 Northampton Town | npower League Two |
| 20 | Sat 23 Feb 2013 | 32-1 v Wycombe WanderersWycombe Wanderers 1-2 Southend United | npower League Two |
| 21 | Tue 26 Feb 2013 | 30-2 v BarnetBarnet 2-0 Southend United | npower League Two |
| 22 | Sat 2 Mar 2013 | 31-1 v Rotherham UnitedSouthend United 1-1 Rotherham United | npower League Two |
| 23 | Sat 9 Mar 2013 | 32-1 v Port ValePort Vale 1-2 Southend United | npower League Two |
| 24 | Tue 12 Mar 2013 | 31-3 v AFC WimbledonSouthend United 1-3 AFC Wimbledon | npower League Two |
| 25 | Sat 16 Mar 2013 | 31-1 v Torquay UnitedSouthend United 1-1 Torquay United | npower League Two |
| 26 | Tue 19 Mar 2013 | 30-2 v Plymouth ArgyleSouthend United 0-2 Plymouth Argyle | npower League Two |
| 27 | Fri 29 Mar 2013 | 32-2 v Bradford CityBradford City 2-2 Southend United | npower League Two |
| 28 | Mon 1 Apr 2013 | 31-1 v Fleetwood TownSouthend United 1-1 Fleetwood Town | npower League Two |
| 29 | Sun 7 Apr 2013 | 30-2 v Crewe AlexandraCrewe Alexandra 2-0 Southend United | Johnstone's Paint Trophy Final |
| 30 | Sat 13 Apr 2013 | 30-0 v Bristol RoversSouthend United 0-0 Bristol Rovers | npower League Two |
| 31 | Tue 16 Apr 2013 | 32-0 v Aldershot TownAldershot Town 0-2 Southend United | npower League Two |
| 32 | Sat 20 Apr 2013 | 31-2 v York CityYork City 2-1 Southend United | npower League Two |
| 33 | Sat 27 Apr 2013 | 30-1 v MorecambeSouthend United 0-1 Morecambe | npower League Two |
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