Ellis was head of recruitment before being promoted into his new role due to an internal restructure.
Reports suggest this came after the appointment of Maurizio Micheli in December as he stepped into a senior recruitment position.
Ellis joins Edu Gaspar, Andrea Berta and Vinai Venkatesham in figures who have left the club over the past year.
Speaking via a lengthy statement on LinkedIn, Ellis waved goodbye to supporters as he thanked the club for their support over the years.
"Time to take the next step…
“I recently departed Arsenal Football Club, where in nearly 5 years I gave my all in an attempt to help contribute to supporting the development of elite level club and its high performance environment.
“I would like to wish the Club the very best for the future.
“Thank you to everyone who has so far in my career, helped shape me, learn so much from and help me find a course that supports my desire to support others, fulfil their potential and support organisations achieve their ambitions.
“I look forward to the next opportunity to continue to do so.”
Per Mertesacker is also set to leave his role as academy manager at the end of the season in what is another staff switch around for The Gunners who certainly aren’t scared of change behind the scenes.