The Croatian, appointed in June to succeed Gian Piero Gasperini after his nine-year tenure, struggled to replicate the form that led to Atalanta finishing third in the standings last season.
They have managed two league wins this campaign and trail leaders Inter Milan by 11 points.
"Atalanta BC announces that Ivan Juric has been relieved of his duties as first team coach," the club said in a statement.
"Atalanta BC would like to thank Ivan Juric and his staff for their hard work and wishes them all the best for the future."
The 50-year-old became AS Roma manager after the sacking of Daniele De Rossi in September 2024, but lasted less than two months in the job before being fired.
He then took charge of Southampton in December of the same year, only to leave the club a day after their relegation from the Premier League.
Former Fiorentina boss Raffaele Palladino has been tipped by local media to be the new manager of Atalanta, who prepare to travel to Napoli on 22 November after the international break.
