Omit day and month for end of season table.
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts |
|---|---|---|---|---|---|---|---|---|---|
| Portsmouth | 46 | 26 | 9 | 11 | 79 | 40 | 39 | 87 | |
| Plymouth Argyle | 46 | 26 | 9 | 11 | 71 | 46 | 25 | 87 | |
| Doncaster Rovers | 46 | 25 | 10 | 11 | 85 | 55 | 30 | 85 | |
| Luton Town | 46 | 20 | 17 | 9 | 70 | 43 | 27 | 77 | |
| Exeter City | 46 | 21 | 8 | 17 | 75 | 56 | 19 | 71 | |
| Carlisle United | 46 | 18 | 17 | 11 | 69 | 68 | 1 | 71 | |
| Blackpool | 46 | 18 | 16 | 12 | 69 | 46 | 23 | 70 | |
| Colchester United | 46 | 19 | 12 | 15 | 67 | 57 | 10 | 69 | |
| Wycombe Wanderers | 46 | 19 | 12 | 15 | 58 | 53 | 5 | 69 | |
| Stevenage | 46 | 20 | 7 | 19 | 67 | 63 | 4 | 67 | |
| Cambridge United | 46 | 19 | 9 | 18 | 58 | 50 | 8 | 66 | |
| Mansfield Town | 46 | 17 | 15 | 14 | 54 | 50 | 4 | 66 | |
| Accrington Stanley | 46 | 17 | 14 | 15 | 59 | 56 | 3 | 65 | |
| Grimsby Town | 46 | 17 | 11 | 18 | 59 | 63 | -4 | 62 | |
| Barnet | 46 | 14 | 15 | 17 | 57 | 64 | -7 | 57 | |
| Notts County | 46 | 16 | 8 | 22 | 54 | 76 | -22 | 56 | |
| Crewe Alexandra | 46 | 14 | 13 | 19 | 58 | 67 | -9 | 55 | |
| Morecambe | 46 | 14 | 10 | 22 | 53 | 73 | -20 | 52 | |
| Crawley Town | 46 | 13 | 12 | 21 | 53 | 71 | -18 | 51 | |
| Yeovil Town | 46 | 11 | 17 | 18 | 49 | 64 | -15 | 50 | |
| Cheltenham Town | 46 | 12 | 14 | 20 | 49 | 69 | -20 | 50 | |
| Newport County | 46 | 12 | 12 | 22 | 51 | 73 | -22 | 48 | |
| Hartlepool United | 46 | 11 | 13 | 22 | 54 | 75 | -21 | 46 | |
| Leyton Orient | 46 | 10 | 6 | 30 | 47 | 87 | -40 | 36 |
| 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 |