| 28. Round | 18/01/2025 | Tamworth FC | - | Boston United | 3:0 | ||||
| 29. Round | 25/01/2025 | Boston United | - | York City | 3:1 |  |
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| 31. Round | 08/02/2025 | Boston United | - | Barnet FC | 0:0 | ||||
| 32. Round | 15/02/2025 | Halifax Town | - | Boston United | 1:0 | ||||
| 33. Round | 18/02/2025 | AFC Fylde | - | Boston United | 1:2 | ||||
| 34. Round | 22/02/2025 | Boston United | - | Eastleigh FC | 1:2 | ||||
| 35. Round | 01/03/2025 | Dagenham & Redbridge | - | Boston United | 1:3 | ||||
| 36. Round | 04/03/2025 | Boston United | - | Oldham Athletic | 0:0 | ||||
| 37. Round | 08/03/2025 | Boston United | - | Woking FC | 2:2 | ||||
| 30. Round | 11/03/2025 | Yeovil Town | - | Boston United | 0:3 | |
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| 38. Round | 15/03/2025 | Braintree Town | - | Boston United | 0:1 | ||||
| 23. Round | 18/03/2025 | Rochdale AFC | - | Boston United | 2:3 | |
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| 39. Round | 22/03/2025 | Hartlepool United | - | Boston United | 4:1 | ||||
| 27. Round | 25/03/2025 | Boston United | - | Southend United | 3:0 | |
 |
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| 40. Round | 29/03/2025 | Boston United | - | Sutton United | 2:1 | ||||
| 25. Round | 01/04/2025 | Wealdstone FC | - | Boston United | 1:0 | ||||
| 44. Round | 21/04/2025 | Solihull Moors | - | Boston United | 3:2 | ||||
| 46. Round | 05/05/2025 | Maidenhead United | - | Boston United | 3:0 |
England