Henen moves to Goodison Park on a simultaneous loan after 41-time Greek champions agreed a deal to sign the 18-year-old from Anderlecht.
The paperwork for the deal was completed late on Monday night and the youngster will join up with Everton’s U21 side after turning out for Belgium's U19s in Serbia during the international break.
Everton boss Roberto Martinez appears to see the player as a long-term prospect though, and is unlikely to rush the player into the first team.
"As we had said previously he's someone whose potential we recognise and at this stage he will go into the Under-21 development squad," said Martinez.
"We're looking forward to working with him this season."
Martinez also tried to bring in Manchester United midfielder Tom Cleverley late on Monday after it became apparent the 25-year-old, in the final 12 months of his contract at Old Trafford, was available.
United had agreed a fee with Aston Villa and the player was set to undergo a medical only for him to become aware of interest from Martinez, who previously had Cleverley on loan for a season while at Wigan.
Hull City were also interested in the player and that created more complications before time ran out on all three clubs to sign the player before the deadline.