Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 06/08/2016 | Plymouth | 0 | 3 | Luton | L Collins |
| 13/08/2016 | Carlisle | 1 | 0 | Plymouth | A Haines |
| 16/08/2016 | Notts County | 1 | 2 | Plymouth | M Heywood |
| 20/08/2016 | Plymouth | 2 | 0 | Mansfield | B Malone |
| 27/08/2016 | Blackpool | 0 | 1 | Plymouth | N Miller |
| 03/09/2016 | Plymouth | 1 | 0 | Cheltenham | N Kinseley |
| 10/09/2016 | Plymouth | 2 | 1 | Cambridge | L Probert |
| 17/09/2016 | Exeter | 0 | 2 | Plymouth | D Whitestone |
| 24/09/2016 | Plymouth | 1 | 1 | Hartlepool | G Ward |
| 27/09/2016 | Leyton Orient | 0 | 2 | Plymouth | C Breakspear |
| 01/10/2016 | Plymouth | 4 | 1 | Yeovil | S Stockbridge |
| 08/10/2016 | Stevenage | 1 | 2 | Plymouth | R Joyce |
| 15/10/2016 | Plymouth | 2 | 2 | Portsmouth | D Handley |
| 22/10/2016 | Newport County | 1 | 3 | Plymouth | M Salisbury |
| 29/10/2016 | Plymouth | 2 | 1 | Colchester | K Johnson |
| 12/11/2016 | Crewe | 1 | 2 | Plymouth | N Miller |
| 19/11/2016 | Plymouth | 0 | 3 | Grimsby | R Jones |
| 22/11/2016 | Plymouth | 0 | 2 | Barnet | B Huxtable |
| 26/11/2016 | Morecambe | 2 | 1 | Plymouth | D England |
| 10/12/2016 | Plymouth | 2 | 0 | Doncaster | O Langford |
| 17/12/2016 | Accrington | 0 | 1 | Plymouth | S Duncan |
| 26/12/2016 | Plymouth | 3 | 3 | Wycombe | G Salisbury |
| 31/12/2016 | Plymouth | 2 | 0 | Crawley Town | B Malone |
| 02/01/2017 | Barnet | 1 | 0 | Plymouth | N Kinseley |
| 14/01/2017 | Plymouth | 4 | 2 | Stevenage | J Busby |
| 21/01/2017 | Cheltenham | 1 | 2 | Plymouth | R Joyce |
| 31/01/2017 | Yeovil | 2 | 1 | Plymouth | K Johnson |
| 04/02/2017 | Cambridge | 0 | 1 | Plymouth | J Brooks |
| 11/02/2017 | Plymouth | 3 | 0 | Exeter | S Hooper |
| 14/02/2017 | Plymouth | 2 | 3 | Leyton Orient | C Sarginson |
| 18/02/2017 | Hartlepool | 1 | 1 | Plymouth | A Haines |
| 25/02/2017 | Luton | 1 | 1 | Plymouth | D Drysdale |
| 28/02/2017 | Plymouth | 0 | 1 | Notts County | G Ward |
| 04/03/2017 | Plymouth | 2 | 0 | Carlisle | M Heywood |
| 07/03/2017 | Plymouth | 0 | 3 | Blackpool | J Busby |
| 11/03/2017 | Mansfield | 0 | 2 | Plymouth | R Clark |
| 14/03/2017 | Wycombe | 1 | 1 | Plymouth | C Breakspear |
| 18/03/2017 | Plymouth | 1 | 0 | Morecambe | D Whitestone |
| 26/03/2017 | Doncaster | 0 | 1 | Plymouth | O Langford |
| 01/04/2017 | Plymouth | 0 | 1 | Accrington | D Deadman |
| 08/04/2017 | Crawley Town | 1 | 2 | Plymouth | B Toner |
| 14/04/2017 | Portsmouth | 1 | 1 | Plymouth | C Sarginson |
| 17/04/2017 | Plymouth | 6 | 1 | Newport County | G Horwood |
| 22/04/2017 | Colchester | 0 | 0 | Plymouth | D Handley |
| 29/04/2017 | Plymouth | 2 | 1 | Crewe | T Kettle |
| 06/05/2017 | Grimsby | 1 | 1 | Plymouth | R Joyce |