| 1 | Tue 8 Jan 2013 | 1-2 v Harrogate TownBoston United 1-2 Harrogate Town | Blue Square Bet North |
| 2 | Sat 12 Jan 2013 | 1-0 v Colwyn BayBoston United 1-0 Colwyn Bay | Blue Square Bet North |
| 3 | Tue 29 Jan 2013 | 1-7 v AltrinchamAltrincham 7-1 Boston United | Blue Square Bet North |
| 4 | Sat 2 Feb 2013 | 2-2 v Gainsborough TrinityGainsborough Trinity 2-2 Boston United | Blue Square Bet North |
| 5 | Sat 9 Feb 2013 | 1-2 v GuiseleyGuiseley 2-1 Boston United | Blue Square Bet North |
| 6 | Sat 2 Mar 2013 | 0-1 v Vauxhall MotorsBoston United 0-1 Vauxhall Motors | Blue Square Bet North |
| 7 | Tue 5 Mar 2013 | 4-0 v Gloucester CityBoston United 4-0 Gloucester City | Blue Square Bet North |
| 8 | Sat 9 Mar 2013 | 2-0 v Brackley TownBrackley Town 0-2 Boston United | Blue Square Bet North |
| 9 | Sat 16 Mar 2013 | 3-0 v Worcester CityWorcester City 0-3 Boston United | Blue Square Bet North |
| 10 | Sat 23 Mar 2013 | 0-4 v Bradford Park AvenueBoston United 0-4 Bradford Park Avenue | Blue Square Bet North |
| 11 | Mon 1 Apr 2013 | 1-1 v Bishop's StortfordBoston United 1-1 Bishop's Stortford | Blue Square Bet North |
| 12 | Sat 13 Apr 2013 | 1-2 v FC Halifax TownBoston United 1-2 FC Halifax Town | Blue Square Bet North |
| 13 | Sat 20 Apr 2013 | 1-1 v HistonHiston 1-1 Boston United | Blue Square Bet North |
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