The Belgian forward joined Olympiakos from Anderlecht on Monday before immediately completing a season-long move to Goodison Park
The Premier League club confirmed the deal on Tuesday morning and said the deal was done before the transfer window closed on Monday night.
The 18-year-old Henen moved from Anderlecht to Olympiakos on Monday before immediately signing a loan deal with the Goodison Park outfit.
Everton boss Roberto Martinez told the club's official website: "As we had said previously, he's someone whose potential we recognised and at this stage he will go into the Under-21 development squad.
"We [are] looking forward to working with him this season."
Henen is a Belgium youth international.