The Wolfsburg assistant coach, who has experience at the Dutch football federation, Barcelona and Bayern Munich, will replace Liam Brady at the end of the season
The 51-year-old, who is currently the assistant manager to Dieter Hecking at Wolfsburg, will succeed Liam Brady at the end of the season.
Jonker has previous experience of coaching youngsters during 10 years, over two spells, at the Dutch football federation, along with temporary spells at the likes of Barcelona and Bayern Munich.
"I am very pleased that Andries is joining us," Arsene Wenger told the club’s official website.
"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."
Arsenal confirmed that Brady will remain associated with the club in ambassadorial role, helping Jonker settle into his new role.