Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 06/08/2016 | Portsmouth | 1 | 1 | Carlisle | G Salisbury |
| 13/08/2016 | Crewe | 0 | 0 | Portsmouth | D Whitestone |
| 16/08/2016 | Morecambe | 2 | 0 | Portsmouth | N Miller |
| 20/08/2016 | Portsmouth | 2 | 0 | Colchester | C Breakspear |
| 27/08/2016 | Exeter | 0 | 1 | Portsmouth | G Ward |
| 03/09/2016 | Portsmouth | 3 | 0 | Crawley Town | B Toner |
| 10/09/2016 | Portsmouth | 4 | 2 | Wycombe | T Robinson |
| 17/09/2016 | Accrington | 1 | 0 | Portsmouth | M Haywood |
| 24/09/2016 | Portsmouth | 5 | 1 | Barnet | D England |
| 27/09/2016 | Blackpool | 3 | 1 | Portsmouth | D Webb |
| 01/10/2016 | Portsmouth | 1 | 2 | Doncaster | D Deadman |
| 08/10/2016 | Leyton Orient | 0 | 1 | Portsmouth | C Sarginson |
| 15/10/2016 | Plymouth | 2 | 2 | Portsmouth | D Handley |
| 22/10/2016 | Portsmouth | 1 | 2 | Notts County | N Miller |
| 29/10/2016 | Cambridge | 0 | 1 | Portsmouth | R Joyce |
| 12/11/2016 | Portsmouth | 4 | 0 | Mansfield | R East |
| 19/11/2016 | Cheltenham | 1 | 1 | Portsmouth | J Brooks |
| 22/11/2016 | Luton | 1 | 3 | Portsmouth | D Coote |
| 26/11/2016 | Portsmouth | 1 | 2 | Stevenage | B Toner |
| 10/12/2016 | Grimsby | 0 | 1 | Portsmouth | A Haines |
| 17/12/2016 | Portsmouth | 0 | 0 | Hartlepool | G Horwood |
| 26/12/2016 | Newport County | 2 | 3 | Portsmouth | C Breakspear |
| 30/12/2016 | Yeovil | 0 | 0 | Portsmouth | C Sarginson |
| 02/01/2017 | Portsmouth | 1 | 0 | Luton | T Robinson |
| 05/01/2017 | Doncaster | 3 | 1 | Portsmouth | J Simpson |
| 14/01/2017 | Portsmouth | 2 | 1 | Leyton Orient | B Huxtable |
| 28/01/2017 | Portsmouth | 0 | 1 | Exeter | D Whitestone |
| 04/02/2017 | Wycombe | 1 | 0 | Portsmouth | G Salisbury |
| 11/02/2017 | Portsmouth | 2 | 0 | Accrington | G Ward |
| 14/02/2017 | Portsmouth | 2 | 0 | Blackpool | D Deadman |
| 18/02/2017 | Barnet | 1 | 1 | Portsmouth | M Brown |
| 25/02/2017 | Carlisle | 0 | 3 | Portsmouth | R Clark |
| 28/02/2017 | Portsmouth | 1 | 1 | Morecambe | S Martin |
| 04/03/2017 | Portsmouth | 0 | 1 | Crewe | J Busby |
| 07/03/2017 | Crawley Town | 0 | 2 | Portsmouth | K Johnson |
| 11/03/2017 | Colchester | 0 | 4 | Portsmouth | D England |
| 14/03/2017 | Portsmouth | 4 | 0 | Grimsby | R Jones |
| 18/03/2017 | Stevenage | 3 | 0 | Portsmouth | M Salisbury |
| 25/03/2017 | Portsmouth | 2 | 1 | Newport County | T Robinson |
| 01/04/2017 | Hartlepool | 0 | 2 | Portsmouth | M Brown |
| 08/04/2017 | Portsmouth | 3 | 1 | Yeovil | G Horwood |
| 14/04/2017 | Portsmouth | 1 | 1 | Plymouth | C Sarginson |
| 17/04/2017 | Notts County | 1 | 3 | Portsmouth | G Salisbury |
| 22/04/2017 | Portsmouth | 2 | 1 | Cambridge | G Ward |
| 29/04/2017 | Mansfield | 0 | 1 | Portsmouth | L Swabey |
| 06/05/2017 | Portsmouth | 6 | 1 | Cheltenham | C Sarginson |