The Byzantine church includes a well-preserved mosaic floor with images of lions, foxes, fish, peacocks and fruits.
Officials say the church was active between the fifth and seventh centuries A.D. The dig's leader, Amir Ganor of the Israel Antiquities Authority, said the floor was "one of the most beautiful mosaics to be uncovered in Israel in recent years."
"It is unique in its craftsmanship and level of preservation," he said.
It had been built on top of another structure, which scholars believe is about 500 years older when the area was inhabited by Jews. There is also a network of tunnels that may have been used by Jewish rebels fighting Roman armies in the 2nd century.
Stone steps lead down from the floor of church to a small burial cave, which scholars suggest might have been venerated as the burial place of the Old Testament prophet Zecharia.
Archaeologists began digging at the site, known as Hirbet Madras, in December.
The Associated Press contributed to this report.