The skull - which was found adorned with a priest's hat - is thought to belong to a priest who once worked in the church in Parndorf in Burgenland, although not much more is known about the finding.
The skull was found in painted tabernacle - a fixed, locked box sometimes found in Christian churches - that was discovered in the wall cavity.
Much of the church was built 300 years ago by baroque architect Lucas von Hildebrandt but parts of it are much older, including dating back to the 12th century.
It was in this section where the skull was found, meaning the find could be up to 900 years old.
According to the local priest who made the discovery Father Franz Borenich, the fact that the skull was wearing a biretta - a hat worn by Roman Catholic clergymen - could mean that he was high up in the church. Alternatively, he could have been some kind of patron saint.
Archaeologists will now study the skull to try and establish its age, with Father Borenich on the search for evidence of a revered priest who may have been buried on the site hundreds of years ago.