Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 06/08/2016 | Cheltenham | 1 | 1 | Leyton Orient | L Probert |
| 13/08/2016 | Leyton Orient | 0 | 1 | Newport County | M Salisbury |
| 16/08/2016 | Leyton Orient | 3 | 0 | Stevenage | B Huxtable |
| 20/08/2016 | Grimsby | 1 | 2 | Leyton Orient | G Salisbury |
| 27/08/2016 | Leyton Orient | 1 | 2 | Mansfield | K Johnson |
| 03/09/2016 | Morecambe | 1 | 2 | Leyton Orient | J Brooks |
| 10/09/2016 | Carlisle | 2 | 2 | Leyton Orient | B Toner |
| 17/09/2016 | Leyton Orient | 0 | 1 | Yeovil | D Deadman |
| 24/09/2016 | Notts County | 3 | 1 | Leyton Orient | B Malone |
| 27/09/2016 | Leyton Orient | 0 | 2 | Plymouth | C Breakspear |
| 01/10/2016 | Barnet | 0 | 0 | Leyton Orient | D Handley |
| 08/10/2016 | Leyton Orient | 0 | 1 | Portsmouth | C Sarginson |
| 15/10/2016 | Leyton Orient | 1 | 2 | Luton | O Yates |
| 22/10/2016 | Hartlepool | 1 | 3 | Leyton Orient | D Webb |
| 29/10/2016 | Leyton Orient | 0 | 2 | Crewe | A Haines |
| 12/11/2016 | Colchester | 0 | 3 | Leyton Orient | D Whitestone |
| 19/11/2016 | Leyton Orient | 1 | 2 | Blackpool | B Malone |
| 22/11/2016 | Leyton Orient | 0 | 1 | Exeter | T Robinson |
| 26/11/2016 | Doncaster | 3 | 1 | Leyton Orient | R Jones |
| 10/12/2016 | Leyton Orient | 1 | 0 | Accrington | D Drysdale |
| 17/12/2016 | Wycombe | 1 | 0 | Leyton Orient | R Lewis |
| 26/12/2016 | Leyton Orient | 3 | 2 | Crawley Town | T Kettle |
| 31/12/2016 | Leyton Orient | 1 | 1 | Cambridge | L Swabey |
| 02/01/2017 | Exeter | 4 | 0 | Leyton Orient | M Salisbury |
| 07/01/2017 | Leyton Orient | 1 | 3 | Barnet | A Haines |
| 14/01/2017 | Portsmouth | 2 | 1 | Leyton Orient | B Huxtable |
| 28/01/2017 | Mansfield | 2 | 0 | Leyton Orient | G Salisbury |
| 04/02/2017 | Leyton Orient | 1 | 2 | Carlisle | G Horwood |
| 07/02/2017 | Leyton Orient | 0 | 1 | Morecambe | J Brooks |
| 11/02/2017 | Yeovil | 1 | 1 | Leyton Orient | D Deadman |
| 14/02/2017 | Plymouth | 2 | 3 | Leyton Orient | C Sarginson |
| 18/02/2017 | Leyton Orient | 2 | 3 | Notts County | B Huxtable |
| 25/02/2017 | Leyton Orient | 0 | 1 | Cheltenham | N Miller |
| 28/02/2017 | Stevenage | 4 | 1 | Leyton Orient | C Breakspear |
| 04/03/2017 | Newport County | 0 | 4 | Leyton Orient | G Ward |
| 11/03/2017 | Leyton Orient | 0 | 3 | Grimsby | L Swabey |
| 14/03/2017 | Accrington | 5 | 0 | Leyton Orient | G Salisbury |
| 18/03/2017 | Leyton Orient | 1 | 4 | Doncaster | C Sarginson |
| 25/03/2017 | Crawley Town | 3 | 0 | Leyton Orient | T Kettle |
| 01/04/2017 | Leyton Orient | 0 | 2 | Wycombe | C Breakspear |
| 08/04/2017 | Cambridge | 3 | 0 | Leyton Orient | N Kinseley |
| 14/04/2017 | Luton | 2 | 2 | Leyton Orient | B Huxtable |
| 17/04/2017 | Leyton Orient | 2 | 1 | Hartlepool | D Whitestone |
| 22/04/2017 | Crewe | 3 | 0 | Leyton Orient | M Brown |
| 29/04/2017 | Leyton Orient | 1 | 3 | Colchester | C Boyeson |
| 06/05/2017 | Blackpool | 3 | 1 | Leyton Orient | D Webb |