| 27. Round | 31/01/2006 | Bristol Rovers | - | Leyton Orient | 3:3 |  |
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| 31. Round | 04/02/2006 | Torquay United | - | Leyton Orient | 2:0 | ||||
| 36. Round | 04/03/2006 | Shrewsbury Town | - | Leyton Orient | 3:3 |  |
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| 37. Round | 11/03/2006 | Leyton Orient | - | Cheltenham Town | 1:0 | ||||
| 38. Round | 18/03/2006 | Rushden & Diamonds FC | - | Leyton Orient | 1:0 | |
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| 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 | ||||
| 46. Round | 06/05/2006 | Oxford United | - | Leyton Orient | 2:3 |
England