The Swede is replacing Steve Bould, whose new role includes taking charge of the under-23 team.
Ljungberg, who played 214 games and scored 46 times for Arsenal, says he is “really excited” to work with Emery.
The former Sweden international was part of Arsenal’s ‘Invincibles’ side under Arsene Wenger.
Since starting his coaching career, 42-year-old Ljungberg has also been in charge of the club’s under-16s squad.
Bould, meanwhile, is to take up a new role back in the academy, which he ran for 11 years before becoming Wenger’s assistant manager in 2012, staying on to work alongside Emery last season.
Arsenal said the changes, which come into effect from 1 July, will help “create a ‘transition team’ which will collectively manage a player’s development through some of the hardest and most challenging periods of their professional lives”.