Sanllehi initially joined Arsenal from Barcelona in February 2018 as head of football relations and was promoted when Ivan Gazidis left the Emirates to join AC Milan last year.
In a statement on behalf of the club's owners, Kroenke Sports & Entertainment, Stan and Josh Kroenke said: "Raul has made a big contribution during his time with us and will always be part of the Arsenal family. We thank him for all his hard work and expertise and wish him every future success."
Speaking on his departure, Sanllehi said: "I’m proud and pleased with the contribution I’ve made at Arsenal over the past three years, and look forward to enjoying the club’s future success. Arsenal is a true footballing institution.
"I am proud to have been part of its history and I thank Stan and Josh Kroenke for this opportunity. Working with Vinai, we have built a top team for the future. Mikel has made an extremely positive impact since his arrival and has formed a strong team with our technical director, Edu.
"The academy is in very safe hands with Per, and Huss Fahmy is a talented and highly-capable leader of our football operations. Personally, I now look forward to taking some time off and spending time with family and friends before setting to work on a new challenge and cheering Arsenal on to great things."
Sanllehi's departure will come as a blow to Arsenal as the club look to rebuild this summer and kickstart Mikel Arteta's revolution at the Emirates, with managing director Venkatesham now leading the club going forward.
"I am thankful to Stan, Josh and the rest of the Arsenal Board for their trust in me. I will miss working closely with my colleague and friend Raul, but I am looking forward to this new challenge," he Venkatesham.
"There is much work to do to return Arsenal to the top of the game where we belong, which is what our fans rightly demand. While this will not happen overnight, I believe we have many of the critical ingredients to do so. There are many positives to build on across the club.
"While football faces uncertainties ahead as a result of the Covid-19 pandemic, I am confident Arsenal will emerge strongly and look forward with confidence."
The Gooner Fanzine put in two calls to Arsenal on Friday afternoon and Saturday morning asking about Sanllehi's possible departure, with club denying he was leaving on both occasions.