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| Transfers |
 Southend United 30,000,000 < > Tottenham Hotspur |
| IMP | < | Felix AFENA-GYAN | CS | GHA | 54 | 2 | 19/01/03 (21) | 82 | | | Southend United | | | | | | | | 1935 | | | |
| HSG | > | Adam WHARTON | CM | ENG | 58 | 81 | 02/06/04 (19) | 90 | 1.82 | 76 | Tottenham Hotspur | | 2990 | | | | 0 | 0 | 3560 | 0 | Y | |
 Sassuolo 3,500,000 < > Morecambe |
| XKE | > | Giorgos KYRIAKOPOULOS | LB | GRE | 62 | 96 | 05/02/96 (28) | 84 | | | Morecambe | | 10660 | | | | 0 | 0 | 2060 | 0 | +1 | |
 Vorskla Poltava 3,750,000 < > Morecambe |
| LEZ | > | Dmytro RIZNYK | Gk | UKR | 60 | 76 | 30/01/99 (25) | 89 | 1.86 | 77 | Morecambe | | 8320 | | | | 0 | 0 | 2145 | 0 | +1 | |
| Bristol Rovers 3,330,000 < > Hull City |
| CHJ | > | Noah OKAFOR | St | SUI | 62 | 93 | 24/05/00 (23) | 83 | 1.85 | 85 | Hull City | | 11260 | | | | 0 | 0 | 5060 | 0 | +4 | |
| JHB | < | Ruben VARGAS | LW/CS | SUI | 62/63 | 96 | 05/08/98 (25) | 78 | 1.74 | 68 | Bristol Rovers | | 16140 | | | | 3 | 0 | 4215 | 0 | | |
| Swindon Town < > 3,750,000 Aston Villa |
| BWA | < | Chris RICHARDS | CB | USA | 62 | 90 | 28/03/00 (24) | 94 | 1.88 | 82 | Swindon Town | | 11960 | | | | 0 | 0 | 2620 | 0 | +4 | |
 Paris SG 435,000 < > Wrexham |
| YNB | > | Senny MAYULU | AM | FRA | 38 | 97 | 17/05/06 (17) | 91 | | | Wrexham | | 170 | | | | 0 | 0 | 205 | 0 | Y | |
| 235,000 < > Stevenage |
| EDY | > | Kiano DYER | DM | ENG | 37 | 76 | 21/11/06 (17) | 89 | | | Stevenage | | 140 | | | | 0 | 0 | 85 | 0 | Y | |
| 235,000 < > Stevenage |
| CKR | > | Tyrique GEORGE | W | ENG | 38 | 96 | 04/02/06 (18) | 89 | | | Stevenage | | 150 | | | | 0 | 0 | 180 | 0 | Y | |
| Cardiff City < > Liverpool |
| TDS | < | SÁVIO Moreira de Oliveira | LW | BRA | 60/62 | 94 | 10/04/04 (20) | 76 | | | Liverpool | | 11820 | | | | 0 | 0 | 5825 | 0 | +1 | (t.41, Cardiff City) |
| THS | < | MARCOS LEONARDO Santos Almeida | St | BRA | 63 | 97 | 02/05/03 (21) | 91 | 1.78 | 71 | Liverpool | | 12060 | | | | 3 | 0 | 7175 | 2 | +1 | (t.41, Cardiff City) |
 Excelsior < > 1,790,000 Cambridge United |
| GGG | < | Joël DROMMEL | Gk | NED | 61 | 15 | 16/11/96 (27) | 82 | 1.93 | 80 | Excelsior | | | | | | | | 2015 | | | |
 San Lorenzo < > 2,450,000 Doncaster Rovers |
| PVS | < | Giuliano SIMEONE Baldini | St | ARG | 54 | 15 | 18/12/02 (21) | 83 | 1.84 | 72 | San Lorenzo | | | | | | | | 1935 | | | |
 Atlético Madrid 1,500,000 < > QPR |
| VMN | > | JOÃO MÁRIO Neto Lopes | RWB/RW | POR | 64 | 94 | 03/01/00 (24) | 87 | 1.78 | 62 | QPR | | 18480 | | | | 0 | 0 | 3490 | 0 | +3 | |
| FXV | < | Marius WOLF | RW/RWB | GER | 63 | 6 | 27/05/95 (28) | 91 | 1.87 | 73 | Atlético Madrid | | | | | | | | 3510 | | | |
 SK Sturm Graz < > 1,640,000 Bolton Wanderers |
| IWB | < | Dijon KAMERI | AM | AUT | 55 | 0 | 20/04/04 (20) | 90 | | | SK Sturm Graz | | | | | | | | 2115 | | | |
| Exeter City 2,500,000 < > Leeds United |
| FWT | > | ARNAU TENAS Ureña | Gk | ESP | 57 | 90 | 30/05/01 (22) | 81 | 1.85 | 75 | Leeds United | | 5220 | | | | 0 | 0 | 1790 | 0 | +4 | |
| 670,000 < > Leeds United |
| BUV | > | Harry HOWELL | AM | ENG | 38 | 97 | 29/09/08 (15) | 94 | | | Leeds United | | 160 | | | | 0 | 0 | 255 | 0 | Y | |
 Defensor 1,800,000 < > Shrewsbury Town |
| DCQ | > | Alan MATTURRO Romero | CB | URU | 54 | 93 | 11/10/04 (19) | 93 | 1.89 | 74 | Shrewsbury Town | | 1670 | | | | 0 | 0 | 1355 | 0 | Y | |
| Preston North End < > 580,000 Cardiff City |
| BBL | < | Mark HARRIS | CS | WAL | 49 | 94 | 29/12/98 (25) | 90 | 1.82 | 75 | Preston North End | | 1390 | | | | 3 | 0 | 585 | 0 | +2 | |
| 100,000 < > Cardiff City |
| DUV | > | Ethan WHEATLEY | CS | ENG | 38 | 84 | 20/01/06 (18) | 90 | | | Cardiff City | | 160 | | | | 0 | 0 | 225 | 0 | Y | |
 Hibernian < > 4,060,000 Accrington Stan. |
| FGN | < | Daniel JAMES | W | WAL | 61 | 12 | 10/11/97 (26) | 91 | 1.80 | 76 | Hibernian | | | | | | | | 2970 | | | |
| Birmingham City 3,700,000 < > Millwall |
| NCG | > | Maximilian MITTELSTÄDT | LB | GER | 64 | 99 | 18/03/97 (27) | 88 | 1.78 | 69 | Millwall | 6.96 | 18180 | | | | 2 | 0 | 2940 | 2 | +4 | |
| 400,000 < > Burnley |
| ZUL | > | Tin PLAVOTIC | DM/CB | CRO | 54 | 80 | 30/06/97 (26) | 94 | 1.97 | 96 | Burnley | | 3610 | | | | 0 | 0 | 690 | 0 | | |
| 720,000 < > Aston Villa |
| WJR | > | Rémy VITA | LB | FRA | 56 | 90 | 01/04/01 (23) | 85 | 1.70 | 66 | Aston Villa | | 3750 | | | | 0 | 0 | 1220 | 0 | | |
| Lausanne 5,730,000 < > Blackburn Rovers |
| TTH | > | Zeki AMDOUNI | CS | SUI | 61 | 83 | 04/12/00 (23) | 89 | 1.83 | 80 | Blackburn Rovers | | 8890 | | | | 0 | 0 | 4375 | 0 | +1 | |
| Capelle 4,270,000 < > Huddersfield Town |
| GRA | > | Arnaut DANJUMA Groeneveld | LW | NED | 62 | 97 | 31/01/97 (27) | 91 | 1.78 | 74 | Huddersfield Town | | 11960 | | | | 0 | 0 | 3235 | 0 | +1 | |
| Loan/transfer listed |
| OAK | - | Hayden HACKNEY | CM | ENG | 57 | 91 | 26/06/02 (21) | 93 | | | Swindon Town | | 3480 | | | T | 0 | 0 | 2580 | 0 | | |
| Released |
| SUV | 16 | Tolaji BOLA | LB/CB | ENG | 45 | 12 | 04/01/99 (25) | 92 | 1.80 | 80 | Chesterfield | | | | | | | | 135 | | | |
| YCO | 25+ | Charlie McCANN | DM | NIR | 43 | 15 | 24/04/02 (22) | 86 | | | Kettering Town | | | | | | | | 145 | | | |
| KJI | 16 | Alex MacDONALD | LM | SCO | 46 | 14 | 14/04/90 (34) | 92 | 1.70 | 71 | Stevenage | | | | | | | | F/t | | | |
| FVA | 16 | C.J. EGAN-RILEY | CB/DM | ENG | 54 | 1 | 02/01/03 (21) | 88 | 1.83 | 70 | Getafe | | | | | | | | 1125 | | | |
| NKC | 16 | Alex SMITHIES | Gk | ENG | 50 | 3 | 05/03/90 (34) | 95 | 1.85 | 84 | Southend United | | | | | | | | 170 | | | |
