| 1 | Sat 18 Aug 2012 | 1-0 v DroylsdenDroylsden 0-1 Boston United | Blue Square Bet North |
| 2 | Tue 21 Aug 2012 | 6-0 v HistonBoston United 6-0 Histon | Blue Square Bet North |
| 3 | Mon 27 Aug 2012 | 0-1 v Bishop's StortfordBishop's Stortford 1-0 Boston United | 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 29 Sep 2012 | 1-2 v Bradford Park AvenueBradford Park Avenue 2-1 Boston United | 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 3 Nov 2012 | 2-1 v Gainsborough TrinityBoston United 2-1 Gainsborough Trinity | Blue Square Bet North |
| 10 | Sat 17 Nov 2012 | 1-3 v GuiseleyBoston United 1-3 Guiseley | Blue Square Bet North |
| 11 | Tue 20 Nov 2012 | 2-2 v Solihull MoorsBoston United 2-2 Solihull Moors | Blue Square Bet North |
| 12 | Sat 1 Dec 2012 | 2-3 v AltrinchamBoston United 2-3 Altrincham | Blue Square Bet North |
| 13 | Sat 8 Dec 2012 | 0-4 v Vauxhall MotorsVauxhall Motors 4-0 Boston United | Blue Square Bet North |
| 14 | Sat 15 Dec 2012 | 5-1 v DroylsdenBoston United 5-1 Droylsden | Blue Square Bet North |
| 15 | Sat 29 Dec 2012 | 3-1 v Oxford CityBoston United 3-1 Oxford City | Blue Square Bet North |
| 16 | Tue 1 Jan 2013 | 1-2 v Corby TownCorby Town 2-1 Boston United | Blue Square Bet North |
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