| # | Players | Clubs | Nationality | GC | More |
|---|---|---|---|---|---|
| 1 | Owain Fon Williams | Stockport County | Wales | 89 | |
| 2 | Steve Mildenhall | Southend United | England | 70 | |
| 3 | Scott Flinders | Hartlepool United | England | 68 | |
| 4 | Willy Gueret | Milton Keynes Dons | France | 67 | |
| 5 | Mikkel Andersen | Bristol Rovers | Denmark | 66 | |
| 6 | Luke Daniels | Tranmere Rovers | England | 62 | |
| 7 | Alex Smithies | Huddersfield Town | England | 58 | |
| 8 | Alex McCarthy | Yeovil Town | England | 55 | |
| 9 | David Lucas | Swindon Town | England | 54 | |
| 10 | Ben Williams | Colchester United | England | 54 | |
| 11 | Scott Shearer | Wycombe Wanderers | Scotland | 51 | |
| 12 | David Forde | Millwall | Republic of Ireland | 50 | |
| 13 | Jamie Jones | Leyton Orient | England | 48 | |
| 14 | Alan Julian | Gillingham | Northern Ireland | 43 | |
| 15 | Kelvin Davis | Southampton | England | 42 | |
| 16 | Adam Collin | Carlisle United | England | 41 | |
| 17 | Robert Elliot | Charlton Athletic | Republic of Ireland | 40 | |
| 18 | Fraser Forster | Bristol Rovers | England | 36 | |
| 19 | Rene Gilmartin | Walsall | Republic of Ireland | 35 | |
| 20 | Paul Jones | Exeter City | England | 32 |
GC = Goals conceded