Omit day and month for end of season table.
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts |
|---|---|---|---|---|---|---|---|---|---|
| Doncaster Rovers | 23 | 14 | 6 | 3 | 40 | 22 | 18 | 48 | |
| Portsmouth | 23 | 14 | 4 | 5 | 48 | 19 | 29 | 46 | |
| Colchester United | 23 | 14 | 4 | 5 | 43 | 27 | 16 | 46 | |
| Plymouth Argyle | 23 | 13 | 3 | 7 | 41 | 29 | 12 | 42 | |
| Luton Town | 23 | 11 | 7 | 5 | 38 | 26 | 12 | 40 | |
| Blackpool | 23 | 10 | 9 | 4 | 40 | 24 | 16 | 39 | |
| Wycombe Wanderers | 23 | 11 | 6 | 6 | 29 | 21 | 8 | 39 | |
| Accrington Stanley | 23 | 10 | 7 | 6 | 36 | 29 | 7 | 37 | |
| Carlisle United | 23 | 10 | 7 | 6 | 34 | 34 | 0 | 37 | |
| Mansfield Town | 23 | 9 | 7 | 7 | 31 | 21 | 10 | 34 | |
| Stevenage | 23 | 11 | 1 | 11 | 42 | 33 | 9 | 34 | |
| Grimsby Town | 23 | 9 | 6 | 8 | 32 | 31 | 1 | 33 | |
| Cambridge United | 23 | 9 | 5 | 9 | 30 | 26 | 4 | 32 | |
| Yeovil Town | 23 | 8 | 8 | 7 | 25 | 24 | 1 | 32 | |
| Crewe Alexandra | 23 | 8 | 7 | 8 | 35 | 26 | 9 | 31 | |
| Cheltenham Town | 23 | 8 | 7 | 8 | 27 | 25 | 2 | 31 | |
| Crawley Town | 23 | 8 | 7 | 8 | 29 | 30 | -1 | 31 | |
| Exeter City | 23 | 8 | 5 | 10 | 36 | 29 | 7 | 29 | |
| Hartlepool United | 23 | 7 | 8 | 8 | 28 | 30 | -2 | 29 | |
| Notts County | 23 | 7 | 7 | 9 | 25 | 30 | -5 | 28 | |
| Barnet | 23 | 6 | 9 | 8 | 27 | 31 | -4 | 27 | |
| Newport County | 23 | 6 | 8 | 9 | 26 | 35 | -9 | 26 | |
| Morecambe | 23 | 6 | 4 | 13 | 24 | 38 | -14 | 22 | |
| Leyton Orient | 23 | 4 | 1 | 18 | 19 | 40 | -21 | 13 |
| 14 May 2017 | Blackpool 3-2 Luton Town | |
| 14 May 2017 | Carlisle United 3-3 Exeter City | |
| 18 May 2017 | Exeter City 3-2 Carlisle United | |
| 18 May 2017 | Luton Town 3-3 Blackpool | |
| 28 May 2017 | Blackpool 2-1 Exeter City |