Thompson died of prostate cancer on 15 October 2008. His death was announced by Dundee United in a statement: "It is with great sadness that Dundee United announce the death of chairman Eddie Thompson, who died today after a long illness borne with great fortitude, much bravery and a dogged determination to carry out his responsibilities at Tannadice for as long as possible."
He is survived by his widow, daughter, son, and four grandchildren. His son-in-law was killed in a road accident on 12 October 2008. His role as Chairman of Dundee United Football Club was taken over by his son Stephen.