After Abba Arikha and Samuel of Nehardea died at the end of the first generation of the Amoraim, along with the designation of Rav Huna as dean Sura, Judah bar Ezekiel went to the city of Pumbedita and had established a new yeshiva there.

Pumbedita Academy was active for about 800 years over the course of the eras of the Amoraim, Savoraim, and Geonim up until the days of Hai Gaon.

One of Pumbedita's Gaons and dean of the Academy, Hai Gaon (approximately in years 988-990), moved the academy to Baghdad because the number of Jews making a living from agriculture was growing smaller and they were migrating to the big cities, mainly to Baghdad (apart from the phenomenon of Jewish emigration out of Babylonia).

Thousands of letters with halachic issues attached were received at Pumbedita, addressed to the heads of the Academy from all around the Jewish diaspora.

Twenty years later, Hezekiah Gaon, by some accounts, was tortured to death by the Muslim Buyid dynasty and Pumbedita Academy closed.