In
| Player | Team | Date | Fee |
|---|---|---|---|
| Alec Cleland | Rangers | 1 July 1998 | Free |
| John Spencer | Queens Park Rangers | 1 July 1998 | £1,500,000 |
| Marco Materazzi | Perugia | 15 July 1998 | £2,500,000 |
| Olivier Dacourt | Strasbourg | 27 July 1998 | £4,000,000 |
| Chris Woods | Burnley | 28 July 1998 | Free |
| John Collins | Monaco | 31 July 1998 | £2,500,000 |
| David Unsworth | Aston Villa | 20 August 1998 | £3,000,000 |
| Steve Simonsen | Tranmere Rovers | 23 September 1998 | £1,000,000 (+£2,300,000 add-ons) |
| Ibrahima Bakayoko | Montpellier | 9 October 1998 | £4,500,000 |
| David Weir | Hearts | 16 February 1999 | £250,000 |
| Peter Degn | Aarhus | 22 February 1999 | £200,000 |
| Kevin Campbell | Trabzonspor | 24 March 1999 | Loan to end of the season |
| Scot Gemmill | Nottingham Forest | 25 March 1999 | £200,000 |
| Total (initial fees only): | £19,650,000 | ||
- Alec Cleland (Rangers) – Deal agreed on 19th May 1998.
- John Spencer (Queens Park Rangers) – Deal agreed on 1st May 1998.
- Chris Woods (Burnley) – Chris Woods joined Everton as a goalkeeping coach but was registered as a player the following month as a back-up goalkeeper.
- David Unsworth (Aston Villa) – David Unsworth joined Everton just a few weeks after signing for Aston Villa.
Out
| Player | Team | Date | Fee |
|---|---|---|---|
| Chris Lane | Released | 1 July 1998 | |
| John O'Toole | Released | 1 July 1998 | |
| Mark Quayle | Released | 1 July 1998 | |
| Neil Holmes | Released | 1 July 1998 | |
| Padraig Drew | Released | 1 July 1998 | |
| Graham Allen | Tranmere Rovers | 28 August 1998 | 1-month loan |
| Graham Allen | Tranmere Rovers | 23 September 1998 | £500,000 |
| Carl Tiler | Charlton Athletic | 29 September 1998 | £700,000 |
| John O'Kane | Burnley | 22 October 1998 | 1-month loan (extended to 2 months) |
| John Spencer | Motherwell | 27 October 1998 | 3-month loan |
| Michael Branch | Manchester City | 29 October 1998 | 1-month loan |
| Duncan Ferguson | Newcastle United | 24 November 1998 | £8,000,000 |
| Gavin McCann | Sunderland | 26 November 1998 | £500,000 |
| Tony Thomas | Motherwell | 17 December 1998 | £150,000 |
| Paul Gerrard | Oxford United | 18 December 1998 | 1-month loan (extended to 3 months) |
| Mickael Madar | Paris Saint-Germain | 29 December 1998 | Free |
| John Spencer | Motherwell | 28 January 1999 | £500,000 |
| Total (initial fees only): | £10,350,000 | ||
- Chris Lane (Released) – Eventually joined Hereford United ahead of the 1998/99 season.
- John O'Toole (Released) – Eventually joined Northwich Victoria in November 1998.
- Mark Quayle (Released) – Eventually joined Notts County in July 1998.
- Neil Holmes (Released) – Eventually joined Guiseley ahead of the 1998/99 season.
- Padraig Drew (Released) – Eventually joined Home Farm Everton ahead of the 1998/99 season.
| Income | £10,350,000 |
| Expenditure | £19,650,000 |
| Net Spend | +£9,300,000 |