Sven Mislintat will leave Arsenal on February 8, the Premier League club have announced.
The German joined the Gunners on December 1, 2017 and will have been in place for less than 14 months when he departs on February 8.
In a statement on their website, Arsenal said Mislintat had "done a truly outstanding job in helping us recruit players who are making a big impact now and will do so even more in the future".
Those players include Pierre-Emerick Aubameyang, who followed Mislintat from Borussia Dortmund to the Emirates Stadium 12 months ago and has excelled since under Unai Emery.
"It's been an amazing experience to work at a great club like Arsenal in what has been a big time of change," Mislintat said.
"I am excited about what the future holds for the club and am looking forward to new challenges for myself."
Appointed by then chief executive Ivan Gazidis, former Borussia Dortmund chief Mislintat's position was speculated over last week.
It had been anticipated he would be a key figure following last May's departure of Arsene Wenger after 22 years as boss.
Mislintat was one of three people, along with Gazidis and Raul Sanllehi, the director of football, who chose Emery as Wenger's successor.
But the upheaval of Gazidis leaving for AC Milan last September and further behind-the-scenes changes are rumoured to have led to his departure.
Arsenal added: "We wish him every success for the future and thank him for his extremely hard work on behalf of Arsenal."
Other players to have joined Arsenal during Mislintat's employment include Henrikh Mykhitarayan, another former Dortmund player, who moved from Manchester United in January 2018 as Alexis Sanchez went in the opposite direction.
Defender Sokratis Papastathopoulos was another arrival from Dortmund, while Lucas Torreira, Bernd Leno and Matteo Guendouzi have all become integral members of Emery's starting XI.
Weekend reports suggested former Arsenal winger Marc Overmars could come into the club as Mislintat's successor.
Additional reporting by the Press Association.
