The term Pagan referred to certain ancient Vulcan beliefs, as well as to persons adhering to those beliefs.

According to Sybok, modern dogma incorrectly considered Sha Ka Ree a myth concocted by Pagans. (Star Trek V: The Final Frontier)

The Rumarie was an ancient Pagan festival, that as of the late 24th century had not been observed for a millennium. (VOY: "Meld")

Pagans of course in reality also exist on Earth, but in Star Trek they were only ever mentioned in Vulcan contexts.