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| Transfers |
 Empoli < > 1,250,000  Coventry City |
| KKM | < | Daniel JEBBISON | CS | ENG | 52 | 10 | 11/07/03 (21) | 83 | | | Empoli | | | | | | | | 1440 | | | |
| 500,000 < > Newcastle United |
| GUX | > | Freddie ISSAKA | CS | WAL | 45 | 95 | 28/07/06 (18) | 92 | | | Newcastle United | | 440 | | | | 0 | 0 | 680 | 0 | Y | |
| 400,000 < > Newcastle United |
| MET | > | Tyler BINDON | CB | NZL | 48 | 91 | 27/01/05 (19) | 89 | | | Newcastle United | | 750 | | | | 0 | 0 | 545 | 0 | Y | |
| Gillingham < > 340,000 Newcastle United |
| YFW | < | Sol BRYNN | Gk | ENG | 48 | 99 | 30/10/00 (24) | 94 | | | Gillingham | | 1340 | | | | 0 | 0 | 375 | 0 | +2 | |
| Tranmere Rovers 3,600,000 < > Stevenage |
| MRW | > | Jordan JAMES | CM | WAL | 57 | 94 | 27/04/04 (20) | 85 | 1.78 | 63 | Stevenage | | 4850 | | | | 2 | 0 | 2830 | 0 | +4 | |
| Derby County < > FC Halifax |
| OLW | < | Mads HERMANSEN | Gk | DEN | 62 | 95 | 11/07/00 (24) | 91 | 1.85 | 80 | FC Halifax | | 10020 | | | | 0 | 0 | 3115 | 0 | +5 | (t.42, Derby County) |
| GXQ | < | Kristian Nökkvi HLYNSSON | CM/AM | ISL | 61 | 99 | 23/01/04 (20) | 93 | 1.79 | 71 | FC Halifax | | 10920 | | | | 1 | 0 | 5045 | 0 | +5 | (t.42, Derby County) |
| Bournemouth < > FC Halifax |
| EAZ | < | Morten FRENDRUP | DM | DEN | 63 | 94 | 07/04/01 (23) | 87 | 1.78 | 63 | FC Halifax | 6.67 | 7010 | | | | 3 | 0 | 3405 | 1 | +2 | (t.42, Bournemouth) |
| UYT | < | Mohammed DARAMY | RW/St | DEN | 62 | 94 | 07/01/02 (23) | 85 | 1.80 | 71 | FC Halifax | | 11260 | | | | 0 | 0 | 4340 | 0 | +2 | (t.42, Bournemouth) |
| Roma < > 3,890,000 Wrexham |
| UTP | < | Federico CHIESA | W/St | ITA | 64 | 1 | 25/10/97 (27) | 91 | 1.75 | 70 | Roma | | | | | | | | 4330 | | | |
| Derby County < > Wrexham |
| MIY | < | ARNAU MARTÍNEZ López | RB/CB | ESP | 63 | 92 | 25/04/03 (21) | 88 | 1.82 | 72 | Wrexham | | 15940 | | | | 2 | 0 | 4165 | 0 | +3 | (t.42, Derby County) |
 Club Brugge 1,400,000 < > QPR |
| TKK | > | Joaquin SEYS | LB | BEL | 52 | 77 | 28/03/05 (19) | 86 | | | QPR | | 1230 | | | | 0 | 0 | 1005 | 0 | Y | |
| Shrewsbury Town 20,000,000 < > Swindon Town |
| UXU | > | Carney CHUKWUEMEKA | CM | ENG | 55 | 77 | 20/10/03 (21) | 85 | | | Swindon Town | | 3820 | 3 | | | 0 | 0 | 1925 | 0 | +4 | |
 Libertad 7,750,000 < > Swindon Town |
| FVM | > | Diego Alexander GÓMEZ Amarilla | CM | PAR | 60 | 95 | 27/03/03 (21) | 88 | 1.83 | 73 | Swindon Town | | 8460 | | | | 0 | 0 | 3995 | 0 | +4 | |
 Yverdon < > 1,770,000 Swindon Town |
| SAP | < | Michail ANTONIO | CS | JAM | 64 | 12 | 28/03/90 (34) | 95 | 1.82 | 74 | Yverdon | | | | | | | | 1285 | | | |
 Partick Thistle 1,100,000 < > Forest Green |
| YZH | > | James PENRICE | LB | SCO | 55 | 78 | 22/12/98 (26) | 92 | 1.77 | 73 | Forest Green | | 3530 | | | | 0 | 0 | 810 | 0 | +4 | |
| Northampton Town 6,400,000 < > Sheffield United |
| UAB | > | Pascal STRUIJK | LB/CB | NED | 60 | 37 | 11/08/99 (25) | 90 | | | Sheffield United | | 8350 | | | | 3 | 0 | 1850 | 0 | +4 | |
| UKF | > | Josh SARGENT | CS | USA | 59 | 91 | 20/02/00 (24) | 90 | 1.85 | 79 | Sheffield United | | 6500 | | | | 2 | 0 | 2890 | 0 | +4 | |
| Northampton Town 6,500,000 < > Sheffield United |
| ZAU | > | Morgan WHITTAKER | RW/St | ENG | 57 | 83 | 07/01/01 (24) | 90 | 1.83 | 69 | Sheffield United | 6.45 | 5470 | | | | 0 | 0 | 1845 | 2 | +4 | |
| GBZ | > | Tommy CONWAY | CS | SCO | 57 | 95 | 06/08/02 (22) | 93 | 1.85 | 79 | Sheffield United | | 4840 | | | | 0 | 0 | 2715 | 1 | +4 | |
| Northampton Town 1,100,000 < > Sheffield United |
| PUZ | > | Rob DICKIE | CB | ENG | 56 | 98 | 03/03/96 (28) | 92 | 1.95 | 88 | Sheffield United | 6.35 | 4440 | | | | 5 | 0 | 825 | 0 | +4 | |
| Dundee United 1,750,000 < > Bradford City |
| RFX | > | Miller THOMSON | RW | SCO | 46 | 80 | 20/07/04 (20) | 93 | | | Bradford City | | 480 | | | | 0 | 0 | 550 | 0 | Y | |
| Reading < > 10,000 Blackburn Rovers |
| ZLP | < | Louie ANNESLEY | CB/DM | GIB | 39 | 95 | 03/05/00 (24) | 91 | | | Reading | 6.64 | 340 | | | | 1 | 0 | 5 | 0 | +4 | |
| Alloa Athletic < > 90,000 Cheltenham Town |
| RKC | < | Euan CAMERON | AM | SCO | 41 | 11 | 12/08/02 (22) | 93 | | | Alloa Athletic | | | | | | | | 175 | | | |
| Tamworth 275,000 < > Reading |
| BSN | > | George MORRISON | RW | SCO | 39 | 97 | 24/10/05 (19) | 89 | | | Reading | | 180 | | | | 0 | 0 | 190 | 0 | Y | |
 Mbombela United < > 490,000 Reading |
| XIF | < | Andy RINOMHOTA | CM | ZIM | 51 | 0 | 21/04/97 (27) | 89 | 1.75 | 64 | Mbombela United | | | | | | | | 595 | | | |
| Colchester United < > Morecambe |
| HUR | < | Kian BEST | LWB | ENG | 49 | 97 | 27/08/05 (19) | 92 | | | Morecambe | | 1030 | | | | 0 | 0 | 640 | 0 | Y | (t.36, Colchester United) |
| Wealdstone < > Morecambe |
| CRA | < | Triston ROWE | RB/CB | ENG | 38 | 82 | 18/05/06 (18) | 93 | | | Morecambe | | 160 | | | | 0 | 0 | 90 | 0 | Y | (t.42, Wealdstone) |
| Leeds United < > Bolton Wanderers | Tribunal [A] |
| GVZ | < | Gavin BAZUNU | Gk | IRL | 60 | 86 | 20/02/02 (22) | 94 | 1.89 | 79 | Bolton Wanderers | 6.64 | 9920 | | | | 0 | 0 | 2750 | 0 | +1 | |
| HFO | < | Batista MENDY | CB/DM | FRA | 61 | 83 | 12/01/00 (25) | 81 | 1.90 | 81 | Bolton Wanderers | | 10120 | 1 | | T | 0 | 0 | 2145 | 0 | +1 | |
| MEL | < | Emre TEZGEL | CS | ENG | 47 | 93 | 19/09/05 (19) | 86 | | | Bolton Wanderers | | 410 | | | | 0 | 0 | 835 | 0 | Y | |
| VFV | > | Alejandro GARNACHO | W | ARG | 64 | 97 | 01/07/04 (20) | 92 | 1.80 | 80 | Leeds United | 7.00 | 17980 | | | | 3 | 0 | 7750 | 2 | | |
 Erzurumspor 965,000 < > Stockport County |
| ZXI | > | Semi AJAYI | CB/DM | NGA | 57 | 73 | 09/11/93 (31) | 94 | 1.93 | 83 | Stockport County | | 4890 | | | | 0 | 0 | 755 | 0 | +1 | |
| Loan/transfer listed |
| PUS | - | Rabbi MATONDO | W/St | WAL | 58 | 94 | 09/09/00 (24) | 90 | 1.75 | 66 | Stevenage | | 5540 | | | T | 0 | 0 | 2140 | 0 | +3 | |
| PGX | - | Chidera EJUKE | LW | NGA | 61 | 97 | 02/01/98 (27) | 93 | 1.76 | 72 | Stevenage | 6.55 | 9550 | | | T | 0 | 0 | 2795 | 4 | +3 | |
| MBI | - | Luke SHAW | LWB | ENG | 64 | 95 | 12/07/95 (29) | 93 | 1.85 | 74 | Bury | | 26720 | | | T | 0 | 0 | 2575 | 0 | | |
| Released |
| WWO | 16 | Chem CAMPBELL | AM | WAL | 49 | 0 | 30/12/02 (22) | 90 | | | Darlington | | | | | | | | 700 | | | |
| MWZ | <25 | Souahilo MEITÉ | DM/CM | FRA | 61 | 0 | 17/03/94 (30) | 88 | 1.87 | 80 | Benfica | | | | | | | | 1535 | | | |
| Loan callbacks |
| HSG | - | Adam WHARTON | CM | ENG | 62 | 92 | 06/02/04 (20) | 92 | 1.82 | 76 | Tottenham Hotspur | 6.75 | 5400 | | | | 0 | 0 | 5825 | 0 | Y | |
