In
| Player | Team | Date | Fee |
|---|---|---|---|
| Scott Spencer | Oldham Athletic | 12 May 2006 | £250,000 |
| Andy Johnson | Crystal Palace | 30 May 2006 | £8,600,000 |
| Joleon Lescott | Wolverhampton Wanderers | 14 June 2006 | £5,000,000 |
| Tim Howard | Manchester United | 1 July 2006 | Season-long loan |
| Manuel Fernandes | Benfica | 31 January 2007 | Loan to end of the season |
| Total (initial fees only): | £13,850,000 | ||
- Tim Howard (Manchester United) – Deal agreed on 9th May 2006.
Out
| Player | Team | Date | Fee |
|---|---|---|---|
| Nigel Martyn | Retired | 8 June 2006 | |
| Johan Troest Davidsen | Skala | July 2006 | 6-month loan |
| Christian Seargeant | Released | 1 July 2006 | |
| Duncan Ferguson | Released | 1 July 2006 | |
| Jay Harris | Released | 1 July 2006 | |
| Li Tie | Released | 1 July 2006 | |
| Paul Hopkins | Released | 1 July 2006 | |
| Sean Wright | Released | 1 July 2006 | |
| Stephen Wynne | Released | 1 July 2006 | |
| Laurence Wilson | Chester City | 1 July 2006 | |
| Kevin Kilbane | Wigan Athletic | 31 August 2006 | £2,000,000 |
| John Ruddy | Stockport County | 13 September 2006 | 1-month loan (extended to 3 months) [recalled] |
| Patrick Boyle | Norwich City | 14 September 2006 | 1-month loan |
| Iain Turner | Crystal Palace | 16 November 2006 | 1-month loan [recalled] |
| David Weir | Rangers | 16 January 2007 | Free |
| Simon Davies | Fulham | 24 January 2007 | £2,500,000 |
| Mark A. Hughes | Northampton Town | 31 January 2007 | £30,000 |
| Bjarni Vidarsson | Bournemouth | 8 February 2007 | 1-month loan |
| John Ruddy | Wrexham | 9 February 2007 | 1-month loan |
| Alan Kearney | Chester City | 15 February 2007 | 1-month loan |
| Iain Turner | Sheffield Wednesday | 23 February 2007 | 1-month loan (extended to 2 months) |
| John Ruddy | Bristol City | 20 April 2007 | 1-week loan |
| Total (initial fees only): | £4,530,000 | ||
- Christian Seargeant (Released) – Eventually joined Connah's Quay Nomads ahead of the 2006/07 season.
- Duncan Ferguson (Released) – Eventually retired.
- Jay Harris (Released) – Eventually joined Accrington Stanley on 2nd August 2006.
- Li Tie (Released) – Eventually joined Sheffield United in July 2006.
- Paul Hopkins (Released) – Eventually joined Waterford on 15th July 2006.
- Stephen Wynne (Released) – Eventually played non-league football at unknown clubs.
- Laurence Wilson (Chester City) – Deal agreed on 11th May 2006.
- John Ruddy (Stockport County) – Everton recalled John Ruddy in November 2006 to provide cover for Tim Howard who was ineligible to play against Manchester United.
- Iain Turner (Crystal Palace) – Iain Turner had his loan spell cut short due to suffering a groin injury.
| Income | £4,530,000 |
| Expenditure | £13,850,000 |
| Net Spend | +£9,320,000 |