In
| Player | Team | Date | Fee |
|---|---|---|---|
| Richard Gough | San Jose Clash | 17 May 1999 | Free |
| Kevin Campbell | Trabzonspor | 13 July 1999 | £3,000,000 |
| Mark Pembridge | Benfica | 5 August 1999 | £800,000 |
| Abel Xavier | PSV Eindhoven | 2 September 1999 | £1,600,000 |
| Tommy Johnson | Celtic | 24 September 1999 | 3-month loan [recalled] |
| Joe-Max Moore | New England Revolution | 3 December 1999 | Free |
| Stephen Hughes | Arsenal | 7 March 2000 | £3,000,000 |
| Mark Hughes | Southampton | 14 March 2000 | Free |
| Total (initial fees only): | £8,400,000 | ||
- Abel Xavier (PSV Eindhoven) – Originally on trial.
- Tommy Johnson (Celtic) – Tommy Johnson's loan spell at Everton ended after 2 months due to injury problems.
Out
| Player | Team | Date | Fee |
|---|---|---|---|
| Adam Eaton | Preston North End | 23 June 1999 | £5,000 |
| Ibrahima Bakayoko | Marseille | 23 June 1999 | £3,800,000 |
| Olivier Dacourt | Lens | 29 June 1999 | £6,500,000 |
| Mick O'Brien | Released | 1 July 1999 | |
| Wayne McDermott | Released | 1 July 1999 | |
| Marco Materazzi | Perugia | 8 July 1999 | £3,000,000 |
| Craig Short | Blackburn Rovers | 2 August 1999 | £1,750,000 (+£350,000 add-ons) |
| John Oster | Sunderland | 5 August 1999 | £1,100,000 |
| David Poppleton | Lincoln City | 6 August 1999 | Undisclosed |
| Tony Grant | Tranmere Rovers | 2 September 1999 | 1-month loan (extended to 2 months) |
| Terry Phelan | Crystal Palace | 22 October 1999 | 1-month loan (extended to 3 months) |
| Danny Cadamarteri | Fulham | 3 November 1999 | 1-month loan |
| Joe McAlpine | Sacked | 4 November 1999 | |
| Joe Parkinson | Retired | 10 November 1999 | |
| Gareth Farrelly | Bolton Wanderers | 12 November 1999 | 1-month loan |
| John O'Kane | Bolton Wanderers | 19 November 1999 | 1-month loan |
| Thomas Myhre | Rangers | 22 November 1999 | 1-month loan |
| Michael Branch | Wolverhampton Wanderers | 23 November 1999 | 1-month loan |
| Andrew Ralph | Tranmere Rovers | December 1999 | Undisclosed |
| Gareth Farrelly | Bolton Wanderers | 17 December 1999 | £250,000 |
| John O'Kane | Bolton Wanderers | 20 December 1999 | Free |
| Tony Grant | Manchester City | 23 December 1999 | £500,000 |
| Michael Branch | Wolverhampton Wanderers | 19 January 2000 | £500,000 (+£125,000 add-ons) |
| Terry Phelan | Fulham | 3 February 2000 | Free |
| Slaven Bilic | Released | 29 February 2000 | |
| Thomas Myhre | Birmingham City | 31 March 2000 | Loan to end of the season |
| Total (initial fees only): | £17,405,000 | ||
- Mick O'Brien (Released) – Eventually joined Torquay United ahead of the 1999/2000 season.
- Wayne McDermott (Released) – Eventually joined Northwich Victoria in December 1999.
- Terry Phelan (Crystal Palace) – Crystal Palace wanted to extend Terry Phelan's loan spell until the end of the season in January, however the Football League blocked the extension because Phelan was 32 years old and the regulations said end-of-season loans are only permitted for players under the age of 23.
- Joe McAlpine (Sacked) – Sacked for breach of club discipline after stealing hubcaps in Glasgow.
- Slaven Bilic (Released) – Eventually joined Hajduk Split on 2nd March 2000.
| Income | £17,405,000 |
| Expenditure | £8,400,000 |
| Net Spend | -£9,005,000 |