The 51-year-old will join the Gunners at the end of the season from German club Wolfsburg, where he is currently working as their assistant manager.
Jonker previously spent seven years developing and implementing youth coaching reforms for the Dutch FA and also spent spells managing Holland's U15 and U21 teams.
He has been part of the backroom staff at Barcelona and Bayern Munich, both times in tandem with Louis van Gaal, and joined Wolfsburg in 2012.
His appointment follows Liam Brady's decision to leave his role of head of youth development and the Irishman will work with Jonker to ensure a smooth transition - Brady is maintaining his association with the Gunners in an ambassadorial role.
Boss Arsene Wenger said: "I am very pleased that Andries is joining us. He has a big reputation in the game and was a key part of the team which developed the structures which are now producing such strong young players in Holland.
"I look forward to working with him. I would also like to thank Liam for his work which has been outstanding over many years."
Chief executive Ivan Gazidis added: "Youth development is a key part of our philosophy at Arsenal and I am delighted that Andries is joining us.
"He has an outstanding track record in developing and identifying young players and creating systems to bring the best out of them. I know he will build on the tremendous work which has been done by Liam and his team over many years."