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| Transfers |
 Hornchurch < > 170,000 Blackpool |
| BSO | < | Koby MOTTOH | W | ENG | 38 | 14 | 31/08/06 (17) | 92 | | | Hornchurch | | | | | | | | 205 | | | |
 Bayern München < > 1,450,000 Wolves |
| CHN | < | Timothée PEMBÉLÉ | CB/RB | FRA | 56 | 0 | 09/09/02 (21) | 81 | | | Bayern München | | | 1 | | | | | 1515 | | | |
 Cambuur 2,150,000 < > Port Vale |
| JMR | > | Rav VAN DEN BERG | CB | NED | 48/55 | 87 | 07/07/04 (19) | 68 | 1.90 | 75 | Port Vale | | 2290 | | | | 0 | 0 | 1570 | 0 | Y | |
| 175,000 < > Swindon Town |
| AHU | > | Josh ROBERTSON | CM | ENG | 36 | 97 | 30/03/05 (18) | 90 | | | Swindon Town | | 130 | | | | 0 | 0 | 120 | 0 | Y | |
| 1,350,000 < > Swindon Town |
| MGH | > | Alfie GILCHRIST | CB | ENG | 45 | 97 | 28/11/03 (20) | 88 | | | Swindon Town | | 470 | | | | 0 | 0 | 295 | 0 | Y | |
 OH Leuven < > 480,000 QPR |
| OYI | < | Alexandro CALUT | LB | BEL | 49 | 14 | 22/04/03 (20) | 79 | 1.80 | 66 | OH Leuven | | | | | | | | 580 | | | |
| Willem II 7,300,000 < > Cardiff City |
| DII | > | Emanuel EMEGHA | CS | NED | 61 | 82 | 03/02/03 (21) | 90 | 1.76 | 63 | Cardiff City | | 9030 | | | | 0 | 0 | 5375 | 0 | +4 | |
| Reading < > 510,000 Cardiff City |
| WQC | < | Ollie DENHAM | CB/RB | WAL | 49 | 96 | 04/05/02 (21) | 92 | | | Reading | | 1590 | | | | 1 | 0 | 520 | 0 | +1 | |
| Brighton & HA 2,000,000 < > Bolton Wanderers |
| KLH | > | Amar DEDIC | RB | BIH | 62 | 94 | 18/08/02 (21) | 85 | 1.80 | 67 | Bolton Wanderers | | 12760 | | | | 2 | 0 | 3610 | 0 | | |
| LMC | < | MATHEUS MARTINELLI Lima | CM | BRA | 59/60 | 95 | 05/10/01 (22) | 79 | 1.76 | 68 | Brighton & HA | | 7860 | | | | 0 | 0 | 3620 | 0 | | |
| MVV 4,000,000 < > Shrewsbury Town |
| TRO | > | Ruben VAN BOMMEL | St | NED | 56 | 99 | 03/08/04 (19) | 89 | | | Shrewsbury Town | | 2430 | | | | 0 | 0 | 3105 | 0 | Y | |
| NUR | < | Lamare BOGARDE | CM | NED | 46 | 5 | 05/01/04 (20) | 79 | | | MVV | | | | | | | | 550 | | | |
| 420,000 < > Gillingham |
| BTX | > | Oskar BUUR | RB | DEN | 54 | 78 | 31/03/98 (25) | 86 | 1.80 | 71 | Gillingham | | 3430 | | | | 0 | 0 | 740 | 0 | | |
| 400,000 < > Gillingham |
| ZUR | > | Liam KITCHING | CB | ENG | 53 | 93 | 01/10/99 (24) | 92 | 1.91 | 80 | Gillingham | | 2690 | | | | 0 | 0 | 670 | 0 | | |
| 110,000 < > Charlton Athletic |
| FMF | > | Marc ROBERTS | CB | ENG | 54 | 98 | 26/07/90 (33) | 94 | 1.83 | 81 | Charlton Athletic | | 2810 | | | | 0 | 0 | 200 | 0 | +1 | |
| Released |
| WRE | 16 | Jamie LAWRENCE | CB | GER | 44 | 14 | 10/11/02 (21) | 82 | | | Barnet | | | | | | | | 215 | | | |
| TYG | 25+ | Kays RUIZ-ATIL | CM | FRA | 46 | 15 | 26/08/02 (21) | 80 | | | AlbinoLeffe | | | | | | | | 490 | | | |
| NHN | 16 | Kgaogelo CHAUKE | CM | ENG | 42 | 8 | 08/01/03 (21) | 91 | | | Burton Albion | | | | | | | | 250 | | | |
| Loan callbacks |
| PEY | - | Antonio NUSA | LW | NOR | 58 | 97 | 17/04/05 (18) | 87 | 1.75 | 67 | FC Halifax | | 3060 | | | | 3 | 0 | 3850 | 1 | Y | |
| QAT | - | Ashley PHILLIPS | CB | ENG | 49 | 95 | 26/06/05 (18) | 95 | | | Tottenham Hotspur | | 900 | | | | 0 | 0 | 700 | 0 | Y | |
| UXU | - | Carney CHUKWUEMEKA | CM | ENG | 57 | 94 | 20/10/03 (20) | 86 | | | Shrewsbury Town | | 2890 | | | | 0 | 0 | 2830 | 0 | Y | |
