| 1 | Tue 9 Aug 2016 | 32-3 v FulhamLeyton Orient 2-3 Fulham | EFL Cup First Round |
| 2 | Tue 30 Aug 2016 | 33-1 v StevenageLeyton Orient 3-1 Stevenage | Checkatrade Trophy Southern Group G |
| 3 | Sat 3 Sep 2016 | 32-1 v MorecambeMorecambe 1-2 Leyton Orient | Sky Bet League Two |
| 4 | Sat 10 Sep 2016 | 32-2 v Carlisle UnitedCarlisle United 2-2 Leyton Orient | Sky Bet League Two |
| 5 | Sat 17 Sep 2016 | 30-1 v Yeovil TownLeyton Orient 0-1 Yeovil Town | Sky Bet League Two |
| 6 | Sat 24 Sep 2016 | 31-3 v Notts CountyNotts County 3-1 Leyton Orient | Sky Bet League Two |
| 7 | Tue 27 Sep 2016 | 30-2 v Plymouth ArgyleLeyton Orient 0-2 Plymouth Argyle | Sky Bet League Two |
| 8 | Sat 1 Oct 2016 | 30-0 v BarnetBarnet 0-0 Leyton Orient | Sky Bet League Two |
| 9 | Sat 8 Oct 2016 | 30-1 v PortsmouthLeyton Orient 0-1 Portsmouth | Sky Bet League Two |
| 10 | Sat 15 Oct 2016 | 31-2 v Luton TownLeyton Orient 1-2 Luton Town | Sky Bet League Two |
| 11 | Sat 22 Oct 2016 | 33-1 v Hartlepool UnitedHartlepool United 1-3 Leyton Orient | Sky Bet League Two |
| 12 | Sat 29 Oct 2016 | 30-2 v Crewe AlexandraLeyton Orient 0-2 Crewe Alexandra | Sky Bet League Two |
| 13 | Sun 6 Nov 2016 | 30-6 v Sheffield UnitedSheffield United 6-0 Leyton Orient | Emirates FA Cup First Round |
| 14 | Sat 12 Nov 2016 | 33-0 v Colchester UnitedColchester United 0-3 Leyton Orient | Sky Bet League Two |
| 15 | Sat 19 Nov 2016 | 31-2 v BlackpoolLeyton Orient 1-2 Blackpool | Sky Bet League Two |
| 16 | Tue 22 Nov 2016 | 30-1 v Exeter CityLeyton Orient 0-1 Exeter City | Sky Bet League Two |
| 17 | Sat 26 Nov 2016 | 31-3 v Doncaster RoversDoncaster Rovers 3-1 Leyton Orient | Sky Bet League Two |
| 18 | Sat 10 Dec 2016 | 31-0 v Accrington StanleyLeyton Orient 1-0 Accrington Stanley | Sky Bet League Two |
| 19 | Sat 17 Dec 2016 | 30-1 v Wycombe WanderersWycombe Wanderers 1-0 Leyton Orient | Sky Bet League Two |
| 20 | Mon 2 Jan 2017 | 30-4 v Exeter CityExeter City 4-0 Leyton Orient | Sky Bet League Two |
| 21 | Sat 7 Jan 2017 | 31-3 v BarnetLeyton Orient 1-3 Barnet | Sky Bet League Two |
| 22 | Sat 28 Jan 2017 | 30-2 v Mansfield TownMansfield Town 2-0 Leyton Orient | Sky Bet League Two |
| 23 | Sat 4 Feb 2017 | 31-2 v Carlisle UnitedLeyton Orient 1-2 Carlisle United | Sky Bet League Two |
| 24 | Sat 11 Feb 2017 | 31-1 v Yeovil TownYeovil Town 1-1 Leyton Orient | Sky Bet League Two |
| 25 | Tue 14 Feb 2017 | 33-2 v Plymouth ArgylePlymouth Argyle 2-3 Leyton Orient | Sky Bet League Two |
| 26 | Sat 18 Feb 2017 | 32-3 v Notts CountyLeyton Orient 2-3 Notts County | Sky Bet League Two |
| 27 | Sat 25 Feb 2017 | 30-1 v Cheltenham TownLeyton Orient 0-1 Cheltenham Town | Sky Bet League Two |
| 28 | Tue 28 Feb 2017 | 31-4 v StevenageStevenage 4-1 Leyton Orient | Sky Bet League Two |
| 29 | Sat 4 Mar 2017 | 34-0 v Newport CountyNewport County 0-4 Leyton Orient | Sky Bet League Two |
| 30 | Sat 11 Mar 2017 | 30-3 v Grimsby TownLeyton Orient 0-3 Grimsby Town | Sky Bet League Two |
| 31 | Tue 14 Mar 2017 | 30-5 v Accrington StanleyAccrington Stanley 5-0 Leyton Orient | Sky Bet League Two |
| 32 | Sat 25 Mar 2017 | 30-3 v Crawley TownCrawley Town 3-0 Leyton Orient | Sky Bet League Two |
| 33 | Sat 1 Apr 2017 | 30-2 v Wycombe WanderersLeyton Orient 0-2 Wycombe Wanderers | Sky Bet League Two |
| 34 | Sat 29 Apr 2017 | 31-3 v Colchester UnitedLeyton Orient 1-3 Colchester United | Sky Bet League Two |
| 35 | Sat 6 May 2017 | 31-3 v BlackpoolBlackpool 3-1 Leyton Orient | Sky Bet League Two |
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