In
| Player | Team | Date | Fee |
|---|---|---|---|
| Harry Clark | Skerton | 30 April 1898 | Free |
| Jack Crelley | Celtic (Liverpool) | 1 May 1898 | Amateur |
| George Eccles Billy Owen | Wolverhampton Wanderers | 1 May 1898 | £295 |
| George Molyneux | Wigan County | 1 May 1898 | Free |
| Talbot Lewis | Bristol City | 1 May 1898 | Free |
| Charlie Harley | Worcester Rovers | 1 May 1898 | Free |
| John Proudfoot | Blackburn Rovers | 2 May 1898 | £200 |
| William Ball | Blackburn Rovers | 19 May 1898 | £40 |
| George Kitchen | Stockport County | 1 June 1898 | Free |
| Wilfred Oldham | Accrington Stanley (1891) | 16 June 1898 | Free |
| Pritchard Marquis | Kirkdale | October 1898 | Free |
| Thomas Crompton | St Helens Recreation | 16 December 1898 | Free |
| Alfred Vaughan | Rhyl | 14 January 1899 | 1-game loan |
| Jack Blythe | Jarrow | 4 February 1899 | £125 |
| Jimmy Settle | Bury | 11 April 1899 | £400 |
| Wilf Toman | Burnley | 11 April 1899 | £300 |
| Bert Sharp Jack Sharp | Aston Villa | 27 April 1899 | £450 |
| Total (initial fees only): | £1,810 | ||
- Harry Clark (Skerton) – Everton had asked Skerton for a possible fee prior to signing Harry Clark but there is no mention of a transfer fee in the minute books or the cash books.
- Jack Crelley (Celtic (Liverpool)) – Signed professional forms on 26th October 1898.
- Pritchard Marquis (Kirkdale) – Transfer completed around 22nd October 1898.
- Alfred Vaughan (Rhyl) – Alfred Vaughan played for Everton in their 2-0 win over Preston North End for a one-off appearance.
Out
| Player | Team | Date | Fee |
|---|---|---|---|
| Peter Meehan | Southampton | May 1898 | £200 |
| George McKinley | Vale of Leven | May 1898 | Free |
| John Gillan | Dumbarton | May 1898 | Free |
| Bob Struthers | Gravesend United | May 1898 | Free |
| James Littlejohn | Released | 1 May 1898 | |
| David Storrier | Celtic | 4 May 1898 | £125 |
| Bill Williams | Blackburn Rovers | May 1898 | £80 |
| Billy Stewart | Bristol City | May 1898 | Undisclosed |
| John Tait Robertson | Southampton | 23 May 1898 | Co-ownership |
| John Cameron | Tottenham Hotspur | 15 June 1898 | Undisclosed |
| Jack Bell | Celtic | 13 August 1898 | £200 |
| Johnny Holt | Reading | 6 October 1898 | Free |
| John Divers | Celtic | 18 October 1898 | £100 |
| Total (initial fees only): | £705 | ||
- Bob Struthers (Gravesend United) – Bob Struthers was on Everton's retained list despite joining Gravesend United and Portsmouth until he moved to Bolton in May 1901.
- James Littlejohn (Released) – Possibly joined Dumbarton.
- Bill Williams (Blackburn Rovers) – Transfer completed around 12th May 1898.
- Billy Stewart (Bristol City) – Transfer completed around 20th May 1898.
- Johnny Holt (Reading) – Everton wanted £300 for Holt but because Holt joined a Southern League club, there cannot be a transfer fee.
| Income | £705 |
| Expenditure | £1,810 |
| Net Spend | +£1,105 |