Omit day and month for end of season table.
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts |
|---|---|---|---|---|---|---|---|---|---|
| Scunthorpe United | 46 | 26 | 13 | 7 | 73 | 35 | 38 | 91 | |
| Bristol City | 46 | 25 | 10 | 11 | 63 | 39 | 24 | 85 | |
| Blackpool | 46 | 24 | 11 | 11 | 76 | 49 | 27 | 83 | |
| Nottingham Forest | 46 | 23 | 13 | 10 | 65 | 41 | 24 | 82 | |
| Yeovil Town | 46 | 23 | 10 | 13 | 55 | 39 | 16 | 79 | |
| Oldham Athletic | 46 | 21 | 12 | 13 | 69 | 47 | 22 | 75 | |
| Swansea City | 46 | 20 | 12 | 14 | 69 | 53 | 16 | 72 | |
| Carlisle United | 46 | 19 | 11 | 16 | 54 | 55 | -1 | 68 | |
| Tranmere Rovers | 46 | 18 | 13 | 15 | 58 | 53 | 5 | 67 | |
| Millwall | 46 | 19 | 9 | 18 | 59 | 62 | -3 | 66 | |
| Doncaster Rovers | 46 | 16 | 15 | 15 | 52 | 47 | 5 | 63 | |
| Port Vale | 46 | 18 | 6 | 22 | 64 | 65 | -1 | 60 | |
| Crewe Alexandra | 46 | 17 | 9 | 20 | 66 | 72 | -6 | 60 | |
| Northampton Town | 46 | 15 | 14 | 17 | 48 | 51 | -3 | 59 | |
| Huddersfield Town | 46 | 14 | 17 | 15 | 60 | 69 | -9 | 59 | |
| Gillingham | 46 | 17 | 8 | 21 | 56 | 77 | -21 | 59 | |
| Cheltenham Town | 46 | 15 | 9 | 22 | 49 | 61 | -12 | 54 | |
| Brighton and Hove Albion | 46 | 14 | 11 | 21 | 49 | 58 | -9 | 53 | |
| AFC Bournemouth | 46 | 13 | 13 | 20 | 50 | 64 | -14 | 52 | |
| Leyton Orient | 46 | 12 | 15 | 19 | 61 | 77 | -16 | 51 | |
| Chesterfield | 46 | 12 | 11 | 23 | 45 | 53 | -8 | 47 | |
| Bradford City | 46 | 11 | 14 | 21 | 47 | 65 | -18 | 47 | |
| Rotherham United | 46 | 13 | 9 | 24 | 58 | 75 | -17 | 38 | |
| Brentford | 46 | 8 | 13 | 25 | 40 | 79 | -39 | 37 |
| 13 May 2006 | Rotherham United were subjected to a ten point Sporting Sanction by the Football League from the start of the 2006-07 season due to entering a Company Voluntary Agreement (CVA). |
| 11 May 2007 | Yeovil Town 0-2 Nottingham Forest | |
| 13 May 2007 | Oldham Athletic 1-2 Blackpool | |
| 18 May 2007 | Nottingham Forest 2-5 Yeovil Town | |
| 19 May 2007 | Blackpool 3-1 Oldham Athletic | |
| 27 May 2007 | Blackpool 2-0 Yeovil Town |