Reports have suggested that the 24-year-old had agreed on a deal with the Spanish side.
Afellay’s contract with PSV Eindhoven is set to expire at the end of the season.
“We have not reached any agreement with any club whatsoever. Not even with Atletico,” Afellay’s agent Rob Jansen said on his website.
“Some of the names in the press are correct, but I do not wish to confirm any one.”