In

• Charlie Parry (Chester St Oswalds) – Transfer completed around 15th April 1889.
• Fred Geary (Notts Rangers) – Transfer completed around 15th May 1889.
• Alec Brady (Renton) – Transfer completed around 19th July 1889. Alec Brady was suspended in September 1889 until 1st May 1890 due to dual registration. He registered with Burnley just before registering with Everton. His suspension had since been reduced to 1st November 1889.
• Andrew Hannah (Renton) – Transfer completed around 19th July 1889.
• Dan Doyle (Bolton Wanderers) – Transfer completed around 19th July 1889.
• Willie Groves (Celtic) – Transfer completed around 19th July 1889.
• Harry Hammond (Edgehill) – May have joined as an amateur, registered as a professional in October 1889.
• Dan Kirkwood (East Stirlingshire) – Transfer completed around 16th September 1889.
• Rob Jamieson (Bootle (1879)) – Rob Jamieson played for Everton in their 3-0 win over Derby County for a one-off appearance.

Out

• Jack W. Angus (Released) – Eventually joined Gainsborough Trinity ahead of the 1889/90 season.
• Joe Davies (Chirk) – It is implied that the co-ownership of Joe Davies between Everton and Chirk has ended as Davies was reported to have returned to Chirk after playing his last match for Everton in May 1889.
• Dave Waugh (Retired) – Became Everton's trainer immediately after retirement.
• Bob Watson (Released) – Eventually joined Gorton Villa ahead of the 1889/90 season.
• Harry Warmby (Released) – Eventually joined Everton Athletic ahead of the 1889/90 season.
• John Keys (Released) – Eventually joined Everton Athletic ahead of the 1889/90 season.
• Walter Brown (Released) – Eventually joined Rossendale ahead of the 1889/90 season.
• William Wilson (Released) – Eventually joined Stanley.
• Nick Ross (Preston North End) – Transfer completed around 3rd May 1889.
• Jack Gordon (Preston North End) – Cancellation occurred around 19th July 1889. After joining Everton, Jack Gordon changed his mind and wanted to return to Everton, but Everton refused to let him. After a court case, Gordon's contract was nullified and he subsequently rejoined Preston North End.
• George Dobson (Southport Central) – Transfer completed around 3rd August 1889.
• Willie Groves (Celtic) – Similar to Jack Gordon, Willie Groves changed his mind after joining Everton from Celtic. Another court case ensued, Groves' contract at Everton was nullified and he subsequently returned to Celtic.