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| Transfers |
 Olympiakos 4,800,000 < >  Doncaster Rovers |
| DKY | > | Christos MOUZAKITIS | CM | GRE | 58 | 86 | 25/12/06 (19) | 91 | | | Doncaster Rovers | | 5540 | | | | 0 | 0 | 3560 | 0 | +3 | |
 Jong Genk 4,200,000 < > Doncaster Rovers |
| XUZ | > | Robin MIRISOLA | CS | BEL | 56 | 62 | 08/12/06 (19) | 89 | 1.82 | 64 | Doncaster Rovers | | 4040 | | | | 0 | 0 | 3105 | 0 | +4 | |
| Fleetwood Town 1,200,000 < > Bury |
| OEW | > | Harry SOUTTAR | CB | AUS | 56 | 99 | 22/10/98 (27) | 94 | 1.98 | 80 | Bury | 6.76 | 3700 | | | | 1 | 0 | 890 | 0 | +4 | |
 Queen's Park 950,000 < > Bury |
| WJY | > | Blair SPITTAL | RWB/RM | SCO | 56 | 77 | 19/12/95 (30) | 94 | 1.83 | 74 | Bury | | 3700 | | | | 0 | 0 | 705 | 0 | +4 | |
 PEC Zwolle 3,600,000 < > Port Vale |
| JMR | > | Rav VAN DEN BERG | CB | NED | 60 | 97 | 07/07/04 (21) | 88 | 1.90 | 75 | Port Vale | | 7860 | | | | 0 | 0 | 2715 | 0 | +4 | |
| Motherwell 2,800,000 < > Torquay United |
| GTD | > | Tawanda MASWANHISE | LW | ZIM | 57 | 94 | 20/11/02 (23) | 92 | 1.80 | 69 | Torquay United | | 4160 | | | | 0 | 0 | 2090 | 0 | +4 | |
| Kilmarnock 450,000 < > Torquay United |
| EVD | > | Ben BRANNAN | CM | SCO | 42 | 87 | 30/01/07 (19) | 91 | | | Torquay United | | 260 | | | | 0 | 0 | 325 | 0 | Y | |
| 710,000 < > Oldham Athletic |
| SEZ | > | Ali AHMED | W | CAN | 55 | 84 | 10/10/00 (25) | 90 | 1.80 | 70 | Oldham Athletic | | 3520 | | | | 0 | 0 | 1285 | 0 | +1 | |
| Released |
| ZTU | <20 | Joe SBARRA | CM/AM | ENG | 42 | 12 | 21/12/98 (27) | 91 | 1.75 | 70 | Peterhead | | | | | | | | 95 | | | |
| YVD | 25+ | Adam THOMPSON | CB | NIR | 41 | 15 | 28/09/92 (33) | 85 | 1.85 | 74 | Enfield Town | | | | | | | | F/t | | | |
| ZGZ | 16 | Jordan BOWERY | CS | SKN | 48 | 9 | 02/07/91 (34) | 94 | 1.85 | 76 | Alès | | | | | | | | 10 | | | |
| GDW | 25+ | Luke JEPHCOTT | CS | WAL | 37 | 1 | 26/01/00 (26) | 86 | 1.78 | 75 | Truro City | | | | | | | | 20 | | | |
| ZPJ | 25+ | Brendan KIERNAN | W | ENG | 39 | 2 | 10/11/92 (33) | 91 | 1.75 | 74 | Canvey Island | | | | | | | | F/t | | | |
| Loan callbacks |
| IHD | - | Guillaume RESTES | Gk | FRA | 64/65 | 94 | 11/03/05 (21) | 79 | 1.86 | 82 | Norwich City | | 8430 | | | | 0 | 0 | 5925 | 0 | Y | |
