Jonker, who is currently assistant manager at Bundesliga side Wolfsburg, will begin his new role on July 1, succeeding club legend Liam Brady.
Wenger paid tribute to Brady's work at the club during his 18-year spell as head of youth development and spoke of his excitement at working with Jonker, who was involved in a similar role with the Dutch Football Association.
"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," Wenger told the club's official website.
"I look forward to working with him. I would also like to thank Liam for his work which has been outstanding over many years."
Arsenal currently lead the way in the Premier League title race, sitting one point above second-placed Manchester City.