In
| Player | Team | Date | Fee |
|---|---|---|---|
| Stuart McCall | Bradford City | 10 June 1988 | £850,000 |
| Pat Nevin | Chelsea | 5 July 1988 | £925,000 |
| Neil McDonald | Newcastle United | 18 July 1988 | £525,000 |
| Tony Cottee | West Ham United | 25 July 1988 | £2,200,000 |
| Jason Kearton | Brisbane Lions | 31 October 1988 | Free |
| Total (initial fees only): | £4,500,000 | ||
- Pat Nevin (Chelsea) – Everton and Chelsea could not agree on a fee for Pat Nevin - Everton wanted to pay £400,000 while Chelsea wanted £1,700,000. 8 days after the transfer was completed, a tribunal ruled that Everton were to pay Chelsea £925,000.
- Neil McDonald (Newcastle United) – Everton and Newcastle United could not agree on a fee for Neil McDonald - Everton wanted to pay £450,000 while Newcastle United wanted £850,000. A week after the transfer was completed, a tribunal ruled that Everton were to pay Newcastle United £525,000.
- Jason Kearton (Brisbane Lions) – Originally on trial.
Out
| Player | Team | Date | Fee |
|---|---|---|---|
| Derek Mountfield | Aston Villa | 26 May 1988 | £450,000 |
| Lee Elliott | Crewe Alexandra | June 1988 | Free |
| Paul Power | Retired | 3 June 1988 | |
| Alan Harper | Sheffield Wednesday | 8 June 1988 | £275,000 |
| Gary Stevens | Rangers | 14 July 1988 | £1,250,000 |
| Alec Chamberlain | Luton Town | 19 July 1988 | £150,000 |
| Mike Stowell | Port Vale | 19 October 1988 | 1-month loan (extended to 2 months) |
| Adrian Heath | Espanyol | 22 November 1988 | £600,000 |
| Tony Ward | Doncaster Rovers | December 1988 | 1-month loan |
| Neil Adams | Oldham Athletic | 13 January 1989 | 1-month loan (extended to 2 months) |
| Peter Reid | Queens Park Rangers | 7 February 1989 | Free |
| Mike Stowell | Wolverhampton Wanderers | 17 March 1989 | 1-month loan |
| Total (initial fees only): | £2,725,000 | ||
- Paul Power (Retired) – Joined Everton's backroom staff as a youth team coach immediately after retirement.
- Mike Stowell (Wolverhampton Wanderers) – Mike Stowell was expected to remain on-loan at Wolverhampton Wanderers until the end of the season, however Neville Southall suffered an eye injury so the loan was not extended.
| Income | £2,725,000 |
| Expenditure | £4,500,000 |
| Net Spend | +£1,775,000 |