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