The 42-year-old Spaniard – who had spells with MK Dons, Charlton Athletic and Sheffield Wednesday as a player – had spent the last two-and-a-half years overseeing Walsall's youth system.
They are now searching for a replacement and have thanked Llera for his efforts.
They wrote in a club statement: "After careful consideration, Miguel has decided to seek a new challenge elsewhere and leaves after two-and-a-half years at the club.
"The club would like to extend thanks to Miguel for all the contributions made during his tenure as academy manager.
"We would also like to wish him well for the future.
"The club will now begin their efforts to find Miguel’s replacement."
Llera's departure comes hot on the heels of defender Ash Taylor's exit by mutual consent.