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