FIFA on Friday refused to ratify the loan transfer of Vadis Odjidja-Ofoe to Everton from Club Brugge.
The Toffees agreed to a late deal a week ago and believed the required documentation had been submitted just before last Friday's deadline.
However, the move required the green light from world football's governing body and a week later FIFA decided not to rubber-stamp the deal for the 23-year-old midfielder.
"The decision comes despite both the Football Association and Premier League giving their full support to the loan agreement and Everton lodging the relevant signed paperwork in advance of the international transfer deadline on August 31," a statement on Everton's official website said.
Everton confirmed the club will consider "all available options" before discussing the issue further.