| 28. Round | 13/01/2024 | Tranmere Rovers | - | Milton Keynes Dons | 1:2 | ||||
| 34. Round | 17/02/2024 | Swindon Town | - | Milton Keynes Dons | 1:2 | ||||
| 27. Round | 20/02/2024 | Milton Keynes Dons | - | Wrexham AFC | 1:1 | ||||
| 35. Round | 24/02/2024 | Milton Keynes Dons | - | Newport County | 3:0 | ||||
| 36. Round | 02/03/2024 | AFC Wimbledon | - | Milton Keynes Dons | 1:0 |  |
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| 21. Round | 05/03/2024 | Mansfield Town | - | Milton Keynes Dons | 1:2 | ||||
| 37. Round | 09/03/2024 | Milton Keynes Dons | - | Salford City | 3:1 | ||||
| 38. Round | 12/03/2024 | Grimsby Town | - | Milton Keynes Dons | 1:0 | ||||
| 39. Round | 16/03/2024 | Milton Keynes Dons | - | Crewe Alexandra | 3:1 | ||||
| 40. Round | 23/03/2024 | Stockport County | - | Milton Keynes Dons | 5:0 | ||||
| 41. Round | 29/03/2024 | Milton Keynes Dons | - | Walsall FC | 5:0 | ||||
| 43. Round | 06/04/2024 | Forest Green Rovers | - | Milton Keynes Dons | 0:2 | ||||
| 44. Round | 13/04/2024 | Milton Keynes Dons | - | Mansfield Town | 1:4 | ||||
| 45. Round | 20/04/2024 | Harrogate Town | - | Milton Keynes Dons | 3:5 | ||||
| 46. Round | 27/04/2024 | Milton Keynes Dons | - | Sutton United | 4:4 |
Ireland