| # | Players | Clubs | Nationality | GC | More |
|---|---|---|---|---|---|
| 1 | Scott Flinders | Hartlepool United | England | 69 | |
| 2 | Trevor Carson | Bury | Northern Ireland | 63 | |
| 3 | Chris Weale | Shrewsbury Town | England | 62 | |
| 4 | Marek Stech | Yeovil Town | Czech Republic | 58 | |
| 5 | Joe Murphy | Coventry City | Republic of Ireland | 58 | |
| 6 | Paul Jones | Crawley Town | England | 56 | |
| 7 | Mark Gillespie | Carlisle United | England | 50 | |
| 8 | Owain Fon Williams | Tranmere Rovers | Wales | 48 | |
| 9 | Simon Moore | Brentford | England | 47 | |
| 10 | Dean Bouzanis | Oldham Athletic | Australia | 45 | |
| 11 | Bartosz Bialkowski | Notts County | Poland | 43 | |
| 12 | Gary Woods | Doncaster Rovers | England | 43 | |
| 13 | Sam Slocombe | Scunthorpe United | England | 42 | |
| 14 | Simon Eastwood | Portsmouth | England | 39 | |
| 15 | Steven Arnold | Stevenage | England | 38 | |
| 16 | Wesley Foderingham | Swindon Town | England | 37 | |
| 17 | David Martin | Milton Keynes Dons | England | 35 | |
| 18 | George Long | Sheffield United | England | 34 | |
| 19 | Mark Cousins | Colchester United | England | 32 | |
| 20 | Alan Martin | Crewe Alexandra | Scotland | 32 |
GC = Goals conceded