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."
Martinez also tried to bring in Manchester United midfielder Tom Cleverley late yesterday after it became apparent the 25-year-old, in the final 12 months of his contract at Old Trafford, was available.
The Red Devils 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 were also interested in the player and that created more complications and ultimately there was not enough time to thrash out a deal before the deadline.
It seems likely, however, that Martinez will rekindle his interest in January when Cleverley could be available for a cut-price fee as his contract enters its last six months.
Source : PA
Source: PA