"Penders, a Belgium Under-19 international, will join Chelsea from next summer after agreeing a contract with the club until 2032," Chelsea said in a statement.
The 19-year-old will remain with Genk for the rest of the season.
He joins a long list of 'keepers on the books of the English club.
Chelsea already have seven senior goalkeepers under contract.
The club's policy of snapping up young talent from around the globe in the two years since a takeover fronted by LA Dodgers co-owner Todd Boehly has been questioned.
Chelsea have over 50 players on their books with many big names not even training with Enzo Maresca's first-team squad.
Raheem Sterling, Romelu Lukaku and Ben Chilwell, who cost the club over £200 million in transfer fees, are among those who have been frozen out and told to find moves before the end of the transfer window.
Chelsea have won two of their first three games under Maresca after losing their season opener 2-0 to Premier League champions Manchester City.
