The 26-year-old's previous deal had been due to expire at the end of next season.
However, under the terms of the new commitment, Cox has tied himself to the Matchroom Stadium until the summer of 2017.
Cox, who joined Orient from Brighton & Hove Albion in 2010, scored 17 goals in his 56 appearances in all competitions last term.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| C | Portsmouth | 46 | 28 | 13 | 5 | 78 | 41 | 37 | 97 |
| P | Derby CountyDerby | 46 | 28 | 8 | 10 | 78 | 37 | 41 | 92 |
| 3 | Bolton WanderersBolton | 46 | 25 | 12 | 9 | 86 | 51 | 35 | 87 |
| 4 | Peterborough UnitedPeterborough | 46 | 25 | 9 | 12 | 89 | 61 | 28 | 84 |
| 5 | Oxford UnitedOxford Utd | 46 | 22 | 11 | 13 | 79 | 56 | 23 | 77 |
| 6 | Barnsley | 46 | 21 | 13 | 12 | 82 | 64 | 18 | 76 |
| 7 | Lincoln CityLincoln | 46 | 20 | 14 | 12 | 65 | 40 | 25 | 74 |
| 8 | Blackpool | 46 | 21 | 10 | 15 | 65 | 48 | 17 | 73 |
| 9 | Stevenage | 46 | 19 | 14 | 13 | 57 | 46 | 11 | 71 |
| 10 | Wycombe WanderersWycombe | 46 | 17 | 14 | 15 | 60 | 55 | 5 | 65 |
| 11 | Leyton Orient | 46 | 18 | 11 | 17 | 53 | 55 | -2 | 65 |
| 12 | Wigan AthleticWigan | 46 | 20 | 10 | 16 | 63 | 56 | 7 | 62 |
| 13 | Exeter CityExeter | 46 | 17 | 10 | 19 | 46 | 61 | -15 | 61 |
| 14 | Northampton TownNorthampton | 46 | 17 | 9 | 20 | 57 | 66 | -9 | 60 |
| 15 | Bristol Rovers | 46 | 16 | 9 | 21 | 52 | 68 | -16 | 57 |
| 16 | Charlton AthleticCharlton | 46 | 11 | 20 | 15 | 64 | 65 | -1 | 53 |
| 17 | Reading | 46 | 16 | 11 | 19 | 68 | 70 | -2 | 53 |
| 18 | Cambridge UnitedCambridge | 46 | 12 | 12 | 22 | 39 | 61 | -22 | 48 |
| 19 | Shrewsbury TownShrewsbury | 46 | 13 | 9 | 24 | 35 | 67 | -32 | 48 |
| 20 | Burton Albion | 46 | 12 | 10 | 24 | 39 | 67 | -28 | 46 |
| R | Cheltenham TownCheltenham | 46 | 12 | 8 | 26 | 41 | 65 | -24 | 44 |
| R | Fleetwood TownFleetwood | 46 | 10 | 13 | 23 | 49 | 72 | -23 | 43 |
| R | Port Vale | 46 | 10 | 11 | 25 | 41 | 74 | -33 | 41 |
| R | Carlisle UnitedCarlisle | 46 | 7 | 9 | 30 | 41 | 81 | -40 | 30 |
| > League One Full Table | |||||||||
