Emery was appointed head coach at Arsenal in 2018 on a two-year deal, succeeding Arsene Wenger after his 22 years in charge of the club.
However, the Spaniard has been sacked after just 18 months in the role "due to results and performances not being at the level required", according to a club statement.
Freddie Ljungberg, former Arsenal midfielder and member of 'The Invincibles', will take charge of the first team while the club searches for a permanent replacement for Emery.
Arsenal director Josh Kroenke said: "Our most sincere thanks go to Unai and his colleagues who were unrelenting in their efforts to get the club back to competing at the level we all expect and demand.
"We wish Unai and his team nothing but future success."