| # | Team | Penalty goals |
|---|---|---|
| 1 | Luton Town | 8 |
| 2 | Plymouth Argyle | 6 |
| 3 | AFC Wimbledon | 5 |
| 4 | Reading | 5 |
| 5 | Lincoln City | 5 |
| 6 | Doncaster Rovers | 5 |
| 7 | Stockport County | 5 |
| 8 | Stevenage | 4 |
| 9 | Mansfield Town | 4 |
| 10 | Peterborough XI | 4 |
| 11 | Rotherham United | 4 |
| 12 | Bradford City | 3 |
| 13 | Huddersfield | 3 |
| 14 | Northampton Town | 3 |
| 15 | Exeter City | 3 |
| 16 | Burton | 3 |
| 17 | Bolton Wanderers | 3 |
| 18 | Blackpool | 2 |
| 19 | Wycombe Wanderers | 2 |
| 20 | Leyton Orient | 2 |
| 21 | Barnsley | 1 |
| 22 | Port Vale | 1 |
| 23 | Cardiff City | 1 |
| 24 | Wigan Athletic | 1 |