The Swede has played a key role under Mikel Arteta - but the former Gunners player has taken the decision to leave the club to further his coaching career.
Confirming his departure on Twitter, Ljungberg said he was grateful to the club for giving him a chance to develop as a coach but now wants to step up his attempts to become a manager.
"I have decided to leave my first team assistant coaching role at Arsenal to progress my management experience," he wrote. "I have been involved with this club on and off since 1998 and am grateful for all the opportunities they have given me both as a player and as a coach.
"I wish Mikel and all the team every success for the season ahead. Thanks also to the fans for their constant support and for always being by my side. I hope we will all meet again soon.