| 1 | Sat 25 Aug 2012 | 1-2 v Hinckley UnitedBoston United 1-2 Hinckley United | Blue Square Bet North |
| 2 | Mon 27 Aug 2012 | 0-1 v Bishop's StortfordBishop's Stortford 1-0 Boston United | Blue Square Bet North |
| 3 | Sat 1 Sep 2012 | 1-3 v WorkingtonBoston United 1-3 Workington | Blue Square Bet North |
| 4 | Tue 4 Sep 2012 | 2-4 v Oxford CityOxford City 4-2 Boston United | Blue Square Bet North |
| 5 | Sat 8 Sep 2012 | 2-0 v Colwyn BayColwyn Bay 0-2 Boston United | Blue Square Bet North |
| 6 | Sat 15 Sep 2012 | 3-2 v ChesterBoston United 3-2 Chester | Blue Square Bet North |
| 7 | Sat 27 Oct 2012 | 1-2 v Worcester CityBoston United 1-2 Worcester City | Blue Square Bet North |
| 8 | Tue 30 Oct 2012 | 1-0 v Stalybridge CelticStalybridge Celtic 0-1 Boston United | Blue Square Bet North |
| 9 | Sat 1 Dec 2012 | 2-3 v AltrinchamBoston United 2-3 Altrincham | Blue Square Bet North |
| 10 | Wed 5 Dec 2012 | 0-1 v Gloucester CityGloucester City 1-0 Boston United | Blue Square Bet North |
| 11 | Sat 8 Dec 2012 | 0-4 v Vauxhall MotorsVauxhall Motors 4-0 Boston United | Blue Square Bet North |
| 12 | Sat 15 Dec 2012 | 5-1 v DroylsdenBoston United 5-1 Droylsden | Blue Square Bet North |
| 13 | Wed 26 Dec 2012 | 1-1 v Corby TownBoston United 1-1 Corby Town | Blue Square Bet North |
| 14 | Sat 29 Dec 2012 | 3-1 v Oxford CityBoston United 3-1 Oxford City | Blue Square Bet North |
| 15 | Tue 1 Jan 2013 | 1-2 v Corby TownCorby Town 2-1 Boston United | Blue Square Bet North |
| 16 | Sat 5 Jan 2013 | 1-1 v WorkingtonWorkington 1-1 Boston United | Blue Square Bet North |
| 17 | Tue 8 Jan 2013 | 1-2 v Harrogate TownBoston United 1-2 Harrogate Town | Blue Square Bet North |
| 18 | Sat 12 Jan 2013 | 1-0 v Colwyn BayBoston United 1-0 Colwyn Bay | Blue Square Bet North |
| 19 | Tue 29 Jan 2013 | 1-7 v AltrinchamAltrincham 7-1 Boston United | Blue Square Bet North |
| 20 | Sat 2 Feb 2013 | 2-2 v Gainsborough TrinityGainsborough Trinity 2-2 Boston United | Blue Square Bet North |
| 21 | Sat 9 Feb 2013 | 1-2 v GuiseleyGuiseley 2-1 Boston United | Blue Square Bet North |
| 22 | Sat 16 Feb 2013 | 2-2 v Stalybridge CelticBoston United 2-2 Stalybridge Celtic | Blue Square Bet North |
| 23 | Tue 26 Feb 2013 | 2-4 v Harrogate TownHarrogate Town 4-2 Boston United | Blue Square Bet North |
| 24 | Sat 2 Mar 2013 | 0-1 v Vauxhall MotorsBoston United 0-1 Vauxhall Motors | Blue Square Bet North |
| 25 | Tue 5 Mar 2013 | 4-0 v Gloucester CityBoston United 4-0 Gloucester City | Blue Square Bet North |
| 26 | Sat 9 Mar 2013 | 2-0 v Brackley TownBrackley Town 0-2 Boston United | Blue Square Bet North |
| 27 | Sat 16 Mar 2013 | 3-0 v Worcester CityWorcester City 0-3 Boston United | Blue Square Bet North |
| 28 | Sat 23 Mar 2013 | 0-4 v Bradford Park AvenueBoston United 0-4 Bradford Park Avenue | Blue Square Bet North |
| 29 | Sat 30 Mar 2013 | 4-2 v Hinckley UnitedHinckley United 2-4 Boston United | Blue Square Bet North |
| 30 | Mon 1 Apr 2013 | 1-1 v Bishop's StortfordBoston United 1-1 Bishop's Stortford | Blue Square Bet North |
| 31 | Sat 6 Apr 2013 | 0-1 v ChesterChester 1-0 Boston United | Blue Square Bet North |
| 32 | Sat 13 Apr 2013 | 1-2 v FC Halifax TownBoston United 1-2 FC Halifax Town | Blue Square Bet North |
| 33 | Sat 20 Apr 2013 | 1-1 v HistonHiston 1-1 Boston United | Blue Square Bet North |
| 34 | Sat 27 Apr 2013 | 3-4 v Brackley TownBoston United 3-4 Brackley Town | Blue Square Bet North |
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