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 | |
| 1 | Birmingham CityBirmingham | 23 | 16 | 5 | 2 | 41 | 17 | 24 | 53 |
| 2 | Wycombe WanderersWycombe | 25 | 15 | 6 | 4 | 50 | 27 | 23 | 51 |
| 3 | Wrexham | 25 | 15 | 6 | 4 | 37 | 18 | 19 | 51 |
| 4 | Huddersfield TownHuddersfield | 24 | 14 | 5 | 5 | 37 | 19 | 18 | 47 |
| 5 | Barnsley | 25 | 12 | 6 | 7 | 39 | 33 | 6 | 42 |
| 6 | Reading | 24 | 12 | 5 | 7 | 39 | 33 | 6 | 41 |
| 7 | Stockport CountyStockport | 25 | 10 | 8 | 7 | 37 | 27 | 10 | 38 |
| 8 | Leyton Orient | 24 | 11 | 4 | 9 | 32 | 22 | 10 | 37 |
| 9 | Mansfield TownMansfield | 23 | 11 | 4 | 8 | 31 | 26 | 5 | 37 |
| 10 | Bolton WanderersBolton | 24 | 11 | 4 | 9 | 36 | 37 | -1 | 37 |
| 11 | Charlton AthleticCharlton | 23 | 9 | 7 | 7 | 27 | 21 | 6 | 34 |
| 12 | Lincoln CityLincoln | 25 | 8 | 8 | 9 | 28 | 30 | -2 | 32 |
| 13 | Rotherham UnitedRotherham | 24 | 8 | 7 | 9 | 24 | 24 | 0 | 31 |
| 14 | Stevenage | 23 | 8 | 7 | 8 | 18 | 20 | -2 | 31 |
| 15 | Exeter CityExeter | 24 | 9 | 4 | 11 | 28 | 31 | -3 | 31 |
| 16 | Blackpool | 24 | 7 | 9 | 8 | 32 | 35 | -3 | 30 |
| 17 | Wigan AthleticWigan | 23 | 7 | 6 | 10 | 21 | 23 | -2 | 27 |
| 18 | Northampton TownNorthampton | 25 | 6 | 8 | 11 | 24 | 39 | -15 | 26 |
| 19 | Peterborough UnitedPeterborough | 24 | 7 | 4 | 13 | 41 | 46 | -5 | 25 |
| 20 | Bristol Rovers | 24 | 7 | 4 | 13 | 22 | 38 | -16 | 25 |
| 21 | Crawley TownCrawley | 23 | 5 | 5 | 13 | 24 | 43 | -19 | 20 |
| 22 | Shrewsbury TownShrewsbury | 24 | 4 | 5 | 15 | 24 | 44 | -20 | 17 |
| 23 | Cambridge UnitedCambridge | 24 | 4 | 5 | 15 | 22 | 43 | -21 | 17 |
| 24 | Burton Albion | 24 | 2 | 8 | 14 | 20 | 38 | -18 | 14 |
| > League One Full Table | |||||||||
