In
| Player | Team | Date | Fee |
|---|---|---|---|
| Steven Pienaar | Borussia Dortmund | 1 July 2008 | £2,050,000 |
| Lars Jacobsen | Free agent | 26 August 2008 | Free |
| Segundo Castillo | Red Star Belgrade | 28 August 2008 | Loan to end of the season |
| Carlo Nash | Wigan Athletic | 1 September 2008 | Free |
| Louis Saha | Manchester United | 1 September 2008 | Undisclosed |
| Marouane Fellaini | Standard Liege | 1 September 2008 | £15,000,000 |
| Jô | Manchester City | 2 February 2009 | Loan to end of the season |
| Seamus Coleman | Sligo Rovers | 4 February 2009 | £60,000 |
| Total (initial fees only): | £17,110,000 | ||
- Steven Pienaar (Borussia Dortmund) – Deal agreed on 28th April 2008.
- Lars Jacobsen (Free agent) – Released by Nurnberg due to injury problems.
Out
| Player | Team | Date | Fee |
|---|---|---|---|
| Aidan Downes | Yeovil Town | 1 July 2008 | Free |
| Bjarni Vidarsson | Twente | 1 July 2008 | Free |
| Darren Dennehy | Port Vale | 1 July 2008 | Free |
| Jamie Jones | Leyton Orient | 1 July 2008 | Free |
| Lee Carsley | Birmingham City | 1 July 2008 | Free |
| Patrick Boyle | Released | 1 July 2008 | |
| Stefan Wessels | Osnabruck | 1 July 2008 | Free |
| Stephen Connor | Released | 1 July 2008 | |
| Andy Johnson | Fulham | 7 August 2008 | £10,500,000 |
| Lee Molyneux | Southampton | 2 January 2009 | Free |
| John Ruddy | Crewe Alexandra | 29 January 2009 | 1-month loan (extended to end of the season) |
| John Paul Kissock | Accrington Stanley | 30 January 2009 | 1-month loan |
| Total (initial fees only): | £10,500,000 | ||
- Aidan Downes (Yeovil Town) – Deal agreed on 21st May 2008.
- Bjarni Vidarsson (Twente) – Deal agreed before Vidarsson's contract at Everton expired after he was set for release.
- Darren Dennehy (Port Vale) – Deal agreed on 28th June 2008.
- Jamie Jones (Leyton Orient) – Deal agreed before Jones' contract at Everton expired after he was set for release.
- Lee Carsley (Birmingham City) – Deal agreed on 18th May 2008.
- Patrick Boyle (Released) – Eventually joined Dumbarton in January 2009.
- Stefan Wessels (Osnabruck) – Deal agreed on 20th June 2008.
- Stephen Connor (Released) – Eventually joined TNS in January 2009.
| Income | £10,500,000 |
| Expenditure | £17,110,000 |
| Net Spend | +£6,610,000 |