A source close to the player, however, told Sky Sports News on Thursday evening that Barkley never underwent a medical at Chelsea.
It was an incredible turn of events in the closing stages of Deadline Day with Sky sources reporting in the afternoon that Tottenham were interested in making a late bid for the England international.
Barkey has yet to feature this season as he continues his recovery from a groin injury.
Everton majority shareholder Farhad Moshiri revealed his surprise on Sky Sports News after the two clubs had agreed a deal for £35m, as well as personal terms.
“We heard from his agent that he changed his mind and wanted to reconsider his position during the January transfer window,” Moshiri said on SSN.
“Technically he will be with us because he is under contract for another year. It’s a big surprise but that is football.”
Barkley is entering the final year of his contract and had told the club he wanted to leave earlier in the summer for “a new challenge”.
Manager Ronald Koeman said at the end of last season that Barkley would be sold if he did not sign a new deal.