Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 06/08/2016 | Northampton | 1 | 1 | Fleetwood Town | A Haines |
| 13/08/2016 | Charlton | 1 | 1 | Northampton | D England |
| 16/08/2016 | Oldham | 0 | 0 | Northampton | S Stockbridge |
| 20/08/2016 | Northampton | 0 | 0 | AFC Wimbledon | N Kinseley |
| 27/08/2016 | Coventry | 1 | 1 | Northampton | J Simpson |
| 04/09/2016 | Northampton | 3 | 2 | Milton Keynes Dons | D Webb |
| 10/09/2016 | Northampton | 2 | 0 | Walsall | G Ward |
| 17/09/2016 | Chesterfield | 3 | 1 | Northampton | R Jones |
| 24/09/2016 | Northampton | 4 | 0 | Southend | R Joyce |
| 27/09/2016 | Swindon | 1 | 3 | Northampton | B Huxtable |
| 01/10/2016 | Northampton | 2 | 3 | Bristol Rvs | G Horwood |
| 08/10/2016 | Scunthorpe | 1 | 1 | Northampton | D Handley |
| 15/10/2016 | Northampton | 1 | 3 | Millwall | B Toner |
| 18/10/2016 | Peterboro | 3 | 0 | Northampton | N Swarbrick |
| 22/10/2016 | Shrewsbury | 2 | 4 | Northampton | T Kettle |
| 29/10/2016 | Northampton | 3 | 2 | Bury | C Boyeson |
| 12/11/2016 | Gillingham | 2 | 1 | Northampton | L Probert |
| 19/11/2016 | Northampton | 0 | 1 | Peterboro | D Bond |
| 22/11/2016 | Bradford | 1 | 0 | Northampton | C Sarginson |
| 26/11/2016 | Northampton | 0 | 1 | Bolton | D Deadman |
| 10/12/2016 | Port Vale | 2 | 3 | Northampton | G Salisbury |
| 17/12/2016 | Northampton | 2 | 3 | Rochdale | E Ilderton |
| 26/12/2016 | Oxford | 0 | 1 | Northampton | J Brooks |
| 31/12/2016 | Sheffield United | 1 | 0 | Northampton | D Drysdale |
| 02/01/2017 | Northampton | 1 | 2 | Bradford | S Duncan |
| 07/01/2017 | Bristol Rvs | 5 | 0 | Northampton | G Ward |
| 14/01/2017 | Northampton | 1 | 2 | Scunthorpe | G Horwood |
| 21/01/2017 | Milton Keynes Dons | 5 | 3 | Northampton | R East |
| 28/01/2017 | Northampton | 3 | 0 | Coventry | L Probert |
| 04/02/2017 | Walsall | 2 | 1 | Northampton | R Jones |
| 11/02/2017 | Northampton | 3 | 1 | Chesterfield | R Clark |
| 14/02/2017 | Northampton | 2 | 1 | Swindon | D Handley |
| 18/02/2017 | Southend | 2 | 2 | Northampton | J Brooks |
| 25/02/2017 | Fleetwood Town | 3 | 0 | Northampton | A Haines |
| 28/02/2017 | Northampton | 1 | 2 | Oldham | B Huxtable |
| 04/03/2017 | Northampton | 2 | 1 | Charlton | B Toner |
| 11/03/2017 | AFC Wimbledon | 0 | 1 | Northampton | N Miller |
| 14/03/2017 | Northampton | 2 | 1 | Port Vale | G Ward |
| 18/03/2017 | Bolton | 2 | 1 | Northampton | R Clark |
| 25/03/2017 | Northampton | 0 | 0 | Oxford | M Jones |
| 01/04/2017 | Rochdale | 1 | 1 | Northampton | R Joyce |
| 08/04/2017 | Northampton | 1 | 2 | Sheffield United | M Heywood |
| 14/04/2017 | Millwall | 3 | 0 | Northampton | G Salisbury |
| 17/04/2017 | Northampton | 1 | 1 | Shrewsbury | C Breakspear |
| 22/04/2017 | Bury | 3 | 0 | Northampton | N Miller |
| 30/04/2017 | Northampton | 0 | 0 | Gillingham | D England |