| Player in | From | Fee | Date |
| Kevin Kilbane | Wigan Athletic | Undisclosed | 15/01 |
| Manucho | Manchester United | Season-long Loan | 16/01 |
| Kamil Zayatte | Young Boys | £2,500,000 | 23/01 |
| Jimmy Bullard | Fulham | £5,000,000 | 23/01 |
| Steven Mouyokolo | Boulogne | Undisclosed | 02/06 |
| Seyi Olofinjana | Stoke City | £3,000,000 | 06/08 |
| Jozy Altidore | Villareal | Season-long Loan | 10/08 |
| Stephen Hunt |
Reading |
£3,500,000 |
13/08 |
| Kamel Ghilas |
Celta Vigo |
Undisclosed |
13/08 |
| Paul McShane | Sunderland | Undisclosed | 30/08 |
| Ibrahima Sonko | Stoke City | Season-long Loan | 01/09 |
| Jan Vennegoor of Hesselink | Celtic | Free transfer | 02/09 |
| Player out | To | Fee | Date |
| Dean Windass | Oldham Athletic | Loan | 09/01 |
| Bill Law | Released | 22/01 | |
| Nicky McNamara | Released | 22/01 | |
| Liam Simpson | Released | 22/01 | |
| Wayne Brown | Leicester City | Season-long Loan | 30/01 |
| Yann Ekra | Panionios Athens | Season-long Loan | 01/02 |
| Tony Warner | Leicester City | Season-long Loan | 13/03 |
| James Bennett | Lincoln City | Season-long Loan | 25/03 |
| John Welsh | Bury | 1-Month Loan | 27/03 |
| Wayne Brown | Leicester City | Undisclosed | 28/04 |
| Joe Lamplough | Released | 07/05 | |
| Matt Plummer | Released | 07/05 | |
| Tom Woodhead | Released | 07/05 | |
| James Bennett | Released | 02/06 | |
| Michael Bridges | Released | 02/06 | |
| Ryan France | Released | 02/06 | |
| John Welsh | Released | 02/06 | |
| Dean Windass | Released | 02/06 | |
| Sam Ricketts |
Bolton Wanderers |
Undisclosed |
25/07 |
| Michael Turner | Sunderland | £4,000,000 | 31/08 |
| Jamie Devitt | Darlington | 1-Month Loan | 15/09 |
| Caleb Folan | Middlesbrough | 3-Month Loan | 17/09 |
| Nathan Doyle | Barnsley | 3-Month Loan | 18/09 |
| Jamie Devitt | Shrewsbury Town | Loan | 21/10 |
| Mark Oxley | Walsall | Loan | 23/10 |
| Bryan Hughes | Derby County | Loan | 23/10 |
| Nicky Featherstone | Grimsby Town | Loan | 19/11 |
| Will Atkinson | Rochdale | 2-Month Loan | 19/11 |