The layout of Philippopolis was revealed between 1965 and 1985. The remains of the synagogue were discovered by archaeologist Elena Kisyakova during archaeological excavations in 1981 near the Central Post Office.

The synagogue was built in the beginning of the 3rd century CE. The synagogue was destroyed during the invasion of the Goths in 250 CE but rebuilt in its original design. The building was destroyed again in the beginning of the 5th century during the persecution of Jews in the Roman Empire. Then, the building was restored and expanded. As part of this second reconstruction, a new mosaic with geometric and floral patterns was laid over the earlier one. The synagogue was abandoned and destroyed in the end of the 6th century CE.

Since 2016, the restored mosaic floor from the synagogue has been on permanent display in the Plovdiv Museum of Archeology.