The 18-year-old had been training with the Toffees until recently but his parent club Anderlecht decided to sell him to Greek side Olympiakos on Monday.
However, Everton struck a deal to bring the youth international back to England for a season-long loan, although the paperwork was not completed until very late in the day.
The club have confirmed the deal has now been ratified by the Premier League and Henen will link up with Everton's Under-21 side after playing for Belgium's Under-19s in Serbia during the international break.
"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 manager Roberto Martinez.
"We're looking forward to working with him this season."
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