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| Transfers |
 Mansfield Town < > 460,000 Oldham Athletic |
| VCJ | < | Micah HAMILTON | AM/W | ENG | 47 | 0 | 13/11/03 (21) | 93 | | | Mansfield Town | | | | | | | | 575 | | | |
 Hibernian < > 1,000,000 Birmingham City |
| JAK | < | Riley McGREE | AM | AUS | 55 | 11 | 02/11/98 (26) | 84 | 1.78 | 73 | Hibernian | | | | | | | | 1210 | | | |
 Reims < > 3,400,000 Sheffield Weds. |
| SFW | < | Benjamin HENRICHS | RWB/RM | GER | 65 | 6 | 23/02/97 (28) | 93 | 1.81 | 77 | Reims | | | | | | | | 3185 | | | |
 Cádiz < > 2,690,000 Sheffield Weds. |
| ELO | < | PAU LÓPEZ Sabata | Gk | ESP | 63 | 11 | 13/12/94 (30) | 91 | 1.89 | 77 | Cádiz | | | | | | | | 2135 | | | |
| Leicester City 10,000,000 < > Manchester United |
| EYF | > | Amadou ONANA | CM | BEL | 65 | 94 | 16/08/01 (23) | 90 | 1.93 | 76 | Manchester United | | 20900 | | | | 1 | 0 | 6680 | 0 | +4 | |
| Hibernian 500,000 < > Manchester United |
| LPA | > | Joe SCALLY | FB/CB | USA | 64 | 79 | 31/12/02 (22) | 91 | 1.84 | 80 | Manchester United | | 17080 | | | | 0 | 0 | 4355 | 0 | +3 | |
| XOZ | < | Teden MENGI | CB | ENG | 59 | 12 | 30/04/02 (23) | 95 | 1.83 | 78 | Hibernian | | | | | | | | 1905 | | | |
| LFG | < | Mathias JENSEN | CM | DEN | 63 | 2 | 01/01/96 (29) | 91 | 1.80 | 68 | Hibernian | | | | | | | | 3275 | | | |
 Samsunspor < > 2,360,000 Preston North End |
| GGJ | < | Emil RIIS Jakobsen | CS | DEN | 56 | 1 | 24/06/98 (26) | 91 | 1.90 | 83 | Samsunspor | | | | | | | | 1640 | | | |
| Monaco 5,000,000 < > Preston North End |
| HVB | > | Soungoutou MAGASSA | CB/DM | FRA | 62 | 84 | 08/10/03 (21) | 88 | 1.88 | 80 | Preston North End | | 10960 | | | | 0 | 0 | 3610 | 0 | +3 | |
| 1,400,000 < > Rochdale |
| YAX | > | Harrison ARMSTRONG | CM | ENG | 49 | 99 | 19/01/07 (18) | 93 | | | Rochdale | | 1220 | | | | 0 | 0 | 1045 | 0 | +1 | |
| Espanyol 4,850,000 < > Manchester City |
| LCU | > | JOAN GARCÍA Pons | Gk | ESP | 61 | 98 | 04/05/01 (24) | 87 | 1.91 | 79 | Manchester City | | 11620 | | | | 0 | 0 | 2705 | 0 | +1 | |
| 325,000 < > Tottenham Hotspur |
| CBG | > | Bendito MANTATO | W | ENG | 38 | 90 | 25/01/08 (17) | 93 | | | Tottenham Hotspur | | 170 | | | | 0 | 0 | 205 | 0 | Y | |
 Benfica 23,000,000 < > Colchester United |
| XXO | > | JOÃO Pedro Gonçalves NEVES | AM/CM | POR | 65 | 96 | 27/09/04 (20) | 86 | 1.74 | 66 | Colchester United | | 20900 | | | | 0 | 0 | 8930 | 0 | +4 | |
| GDX | < | Joe WILLOCK | CM/AM | ENG | 63 | 1 | 20/08/99 (25) | 92 | 1.83 | 71 | Benfica | | | | | | | | 4215 | | | |
| Middlesbrough 3,000,000 < > Colchester United |
| FUF | > | Maximilian BEIER | St | GER | 64 | 94 | 17/10/02 (22) | 88 | 1.83 | 70 | Colchester United | 6.52 | 18180 | | | | 8 | 0 | 7515 | 4 | +4 | |
| FNB | < | Maurits KJÆRGAARD | CM | DEN | 61 | 96 | 26/06/03 (21) | 90 | 1.89 | 70 | Middlesbrough | 6.50 | 10920 | | | | 2 | 0 | 4615 | 0 | +1 | |
| JCU | < | Eddie NKETIAH | CS | ENG | 62 | 80 | 30/05/99 (26) | 93 | 1.80 | 72 | Middlesbrough | 6.36 | 12460 | | | | 1 | 1 | 4005 | 1 | +1 | |
| Aston Villa 3,500,000 < > Sunderland |
| RDO | < | Yves BISSOUMA | CM | MLI | 65 | 32 | 30/08/96 (28) | 94 | 1.81 | 78 | Aston Villa | | 21100 | 7 | | | 2 | 0 | 4690 | 0 | +1 | |
| TOR | > | Rayan CHERKI | AM/RW | FRA | 63 | 94 | 17/08/03 (21) | 89 | 1.76 | 70 | Sunderland | 6.89 | 14540 | | | | 3 | 2 | 6145 | 1 | +3 | |
 Padova 1,300,000 < > Sunderland |
| DVJ | > | Giovanni LEONI | CB | ITA | 51 | 79 | 21/12/06 (18) | 86 | | | Sunderland | | 1160 | | | | 0 | 0 | 945 | 0 | Y | |
| Sevilla < > 1,580,000 Notts County |
| SEP | < | Yira SOR | LW | NGA | 56 | 2 | 24/07/00 (24) | 92 | 1.74 | 68 | Sevilla | | | | | | | | 1590 | | | |
| 1,195,000 < > Fleetwood Town |
| MEB | > | EOM Ji-sung | LW | KOR | 57 | 76 | 09/05/02 (23) | 90 | 1.77 | 69 | Fleetwood Town | | 4290 | | | | 0 | 0 | 2090 | 0 | +1 | |
| Loan/transfer listed |
| NVJ | - | Kwadwo BAAH | St | GER | 54 | 97 | 27/01/03 (22) | 85 | 1.83 | 75 | Crystal Palace | | 1250 | | | T | 0 | 0 | 1745 | 0 | +3 | |
| MEN | - | Jesuran RAK-SAKYI | LW | ENG | 56 | 93 | 05/10/02 (22) | 89 | | | Crystal Palace | | 3080 | | | T | 3 | 0 | 2015 | 0 | +3 | |
| VEI | - | Jordan STOREY | CB | ENG | 57 | 94 | 02/09/97 (27) | 95 | 1.88 | 75 | Preston North End | | 5140 | | | T | 3 | 0 | 1040 | 0 | +1 | |
| YUW | - | Adam WEBSTER | CB | ENG | 62 | 54 | 04/01/95 (30) | 94 | 1.85 | 74 | Colchester United | 6.42 | 15540 | 1 | | T | 10 | 1 | 1785 | 0 | | |
| YEC | - | Saël KUMBEDI Nseke | RB | FRA | 59/61 | 94 | 26/03/05 (20) | 76 | | | Colchester United | | 5600 | | | T | 0 | 0 | 3425 | 0 | Y | |
| UYS | - | Calum CHAMBERS | RB/CB | ENG | 58 | 94 | 20/01/95 (30) | 93 | 1.82 | 66 | Colchester United | 6.50 | 7110 | | | T | 1 | 0 | 970 | 0 | | |
| XPK | - | Antoni MILAMBO | AM | NED | 49/61 | 94 | 03/04/05 (20) | 60 | 1.79 | 68 | Colchester United | 6.20 | 670 | | | T | 0 | 0 | 5045 | 0 | Y | |
| XGR | - | El Chadaille BITSHIABU | CB | FRA | 60 | 89 | 16/05/05 (20) | 82 | 1.96 | 95 | Colchester United | 6.33 | 2210 | | | T | 1 | 0 | 2970 | 0 | Y | |
| RFE | - | Kees SMIT | CM | NED | 53/55 | 95 | 21/01/06 (19) | 76 | 1.80 | 66 | Colchester United | | 880 | | | T | 0 | 0 | 2305 | 0 | Y | |
| Released |
| YHL | 16 | Danny GARDNER | CS | ENG | 38 | 9 | 30/11/89 (35) | 91 | 1.85 | 79 | Oldham Athletic | | | | | | | | F/t | | | |
| YHJ | 25+ | Kieren FLAVELL | Gk | ENG | 43 | 2 | 21/09/03 (21) | 95 | | | Woking | | | | | | | | 215 | | | |
| YFY | 16 | Sam HUGHES | CB/DM | ENG | 46 | 12 | 15/04/97 (28) | 92 | | | Montrose | | | 26 | | | | | 120 | | | |
| Loan callbacks |
| KCT | - | Samuel Omorodion Aghehowa, SAMU | CS | ESP | 64 | 97 | 05/05/04 (21) | 89 | 1.93 | 90 | Liverpool | 6.87 | 8940 | | | | 3 | 0 | 8285 | 16 | +1 | |
| FYE | - | Sepp VAN DEN BERG | CB | NED | 63 | 99 | 20/12/01 (23) | 94 | 1.90 | 78 | Liverpool | 6.59 | 10920 | | | | 0 | 0 | 3405 | 1 | | |
| DNT | - | Javier Guerra Moreno, JAVI GUERRA | CM/DM | ESP | 62 | 93 | 13/05/03 (22) | 90 | 1.87 | 77 | Tottenham Hotspur | 6.92 | 12960 | | | | 2 | 0 | 4830 | 1 | +1 | |
| HBU | - | Aaron HICKEY | WB | SCO | 61 | 94 | 10/06/02 (22) | 82 | 1.85 | 72 | Manchester City | | 14260 | | | | 1 | 0 | 2840 | 0 | +1 | |
| STI | - | Kenan YILDIZ | LW/AM | TUR | 63 | 95 | 04/05/05 (20) | 92 | 1.87 | 77 | Tottenham Hotspur | 6.70 | 13360 | | | | 2 | 0 | 6720 | 1 | +2 | |
| DWX | - | Rico LEWIS | RWB/DM | ENG | 64 | 97 | 21/11/04 (20) | 95 | 1.75 | 70 | Manchester City | 7.00 | 9470 | | | | 3 | 0 | 5230 | 1 | Y | |
| KRK | - | Roony BARDGHJI | RW/AM | SWE | 56 | 98 | 15/11/05 (19) | 92 | | | Liverpool | 6.88 | 3630 | | | | 2 | 0 | 2665 | 2 | Y | |
| GVZ | - | Gavin BAZUNU | Gk | IRL | 59 | 89 | 20/02/02 (23) | 95 | 1.89 | 79 | Liverpool | 7.03 | 12020 | | | | 1 | 0 | 2210 | 0 | +1 | |
| UXU | - | Carney CHUKWUEMEKA | CM | ENG | 55 | 97 | 20/10/03 (21) | 93 | | | Manchester City | 6.71 | 5660 | | | | 1 | 0 | 1925 | 0 | +1 | |
