The former defender has been the Gunners’ academy manager since 2018, but will relinquish the role at the end of the season.
“Arsenal is and will always be a very special club to me, so this was a difficult decision” Mertesacker told Arsenal’s official website.
“I am very thankful for the trust the club put in me when transitioning from a first-team player directly into the role as Head of Academy. Now it is time for me to move on and explore something new and push myself even further.
“I remain focused on finishing the season strongly, continuing to nurture and develop our young talent and support a seamless transition until my very last day with the club.”