| Player in | From | Fee | Date |
| John Welsh | Liverpool | Exchange deal | 02/01/2006 |
| Sam Collins | Port Vale | £65,000 | 02/01/2006 |
| Billy Paynter | Port Vale | £150,000 | 02/01/2006 |
| Darryl Duffy | Falkirk | Undisclosed | 10/01/2006 |
| Jon Parkin | Macclesfield Town | Undisclosed | 12/01/2006 |
| Alan Rogers | Nottingham Forest | Season-long loan | 20/01/2006 |
| Mark Noble | West Ham United | Season-long loan | 06/02/2006 |
| Rui Marques | Leeds United | Season-long loan | 23/03/2006 |
| Michael Turner | Brentford | £350,000 | 05/07/2006 |
| Dean Marney | Tottenham Hotspur | Undisclosed | 14/07/2006 |
| Sam Ricketts | Swansea City | £300,000 | 14/07/2006 |
| David Livermore | Leeds United | Undisclosed | 01/08/2006 |
| Mark Yeates | Tottenham Hotspur | Loan | 09/08/2006 |
| Nicky Forster | Ipswich Town | £250,000 | 31/08/2006 |
| Michael Bridges | Carlisle United | £325,000 | 31/08/2006 |
| Danny Mills | Manchester City | 2-month loan | 14/09/2006 |
| Jason Jarrett | Preston North End | 1-month loan | 02/11/2006 |
| Player out | To | Fee | Date |
| Paul Anderson | Liverpool | Exchange deal | 02/01/2006 |
| Roland Edge | Released | 06/01/2006 | |
| Marc Joseph | Blackpool | Loan | 10/01/2006 |
| Marc Joseph | Blackpool | Free | 11/01/2006 |
| Matt Duke | Wycombe Wanderers | Loan | 12/01/2006 |
| Jason Price | Doncaster Rovers | £25,000 | 24/01/2006 |
| Curtis Woodhouse | Grimsby Town | Free | 27/01/2006 |
| Sergio Leite | Released | 24/02/2006 | |
| Robbie Stockdale | Darlington | 1-month loan | 24/02/2006 |
| Robbie Stockdale | Tranmere Rovers | Free | 22/06/2006 |
| Kevin Ellison | Tranmere Rovers | £50,000 | 22/06/2006 |
| Scott Wiseman | Rotherham United | Loan | 30/06/2006 |
| Leon Cort | Crystal Palace | £1,250,000 | 30/06/2006 |
| Curtis Aspden | Scarborough | Loan | 01/08/2006 |
| Billy Paynter | Southend United | Loan | 04/08/2006 |
| Billy Paynter | Southend United | £200,000 | 07/08/2006 |
| Mark Lynch | Yeovil Town | 1-month loan | 22/08/2006 |
| Russell Fry | Halifax Town | 1-month loan | 25/08/2006 |
| Tom Matthews | Halifax Town | 1-month loan | 25/08/2006 |
| Keith Andrews | Milton Keynes Dons | Free transfer | 30/08/2006 |
| Ben Burgess | Blackpool | £100,000* | 31/08/2006 |
| Mark Lynch | Yeovil Town | Free transfer | 31/08/2006 |
| Stuart Green | Crystal Palace | £75,000 | 31/08/2006 |
| Michael Byron | Hinckley United | 2-month loan | 01/10/2006 |
| Tom Matthews | Halifax Town | 1-month loan | 10/10/2006 |
| Alton Thelwell | Leyton Orient | 3-month loan | 18/10/2006 |
| Darryl Duffy | Hartlepool United | 2-month loan | 02/11/2006 |
| Ben Wilkinson | Harrogate Town | 1-month loan | 09/12/2006 |
| Russell Fry | Hinckley United | 1-month loan | 12/12/2006 |
* Burgess fee an initial £25,000 and extra £75,000 after 30th appearance for Blackpool.