The 19-year-old spent last season on loan at Goodison Park from the Greek champions and now returns on a three-year contract.
Henen was a regular in David Unsworth???s U21 side in 2014/15 and chipped in with six goals.
He is now keen to continue his football development and feels he can do so under the guidance of Unsworth and first team boss Roberto Martinez.
???I am so happy. Everton are a big club and I feel I can develop here,??? Henen told Everton???s official website.
???For a young player it is the best club because they try to develop youngsters. It is perfect for me.”