| 31. Round | 04/02/2006 | Torquay United | - | Leyton Orient | 2:0 | ||||
| 32. Round | 11/02/2006 | Leyton Orient | - | Carlisle United | 0:0 | ||||
| 33. Round | 14/02/2006 | Northampton Town | - | Leyton Orient | 1:1 | ||||
| 34. Round | 18/02/2006 | Chester City | - | Leyton Orient | 0:2 |  |
 |
||
| 35. Round | 25/02/2006 | Leyton Orient | - | Darlington FC | 1:0 | ||||
| 30. Round | 28/02/2006 | Leyton Orient | - | Barnet FC | 0:0 | ||||
| 36. Round | 04/03/2006 | Shrewsbury Town | - | Leyton Orient | 3:3 | |
|||
| 37. Round | 11/03/2006 | Leyton Orient | - | Cheltenham Town | 1:0 | |
|||
| 38. Round | 18/03/2006 | Rushden & Diamonds FC | - | Leyton Orient | 1:0 | ||||
| 39. Round | 25/03/2006 | Leyton Orient | - | Wycombe Wanderers | 1:0 | |
|||
| 40. Round | 01/04/2006 | Notts County | - | Leyton Orient | 1:1 | ||||
| 41. Round | 08/04/2006 | Leyton Orient | - | Boston United | 2:0 | |
|||
| 42. Round | 15/04/2006 | Mansfield Town | - | Leyton Orient | 0:1 | |
|||
| 43. Round | 17/04/2006 | Leyton Orient | - | Grimsby Town | 0:0 | ||||
| 44. Round | 22/04/2006 | Lincoln City | - | Leyton Orient | 1:1 | ||||
| 45. Round | 29/04/2006 | Leyton Orient | - | Peterborough United | 2:1 |  |
England