The name Zupaysaurus is composed of the Quechua word supay meaning "devil" and the Greek word sauros (σαυρος) meaning "lizard"; thus "devil lizard". In Incan mythology, supay was both the god of death and ruler of the ukhu pacha, the Incan underworld. The type species was named Z. rougieri in the honor of Guillermo Rougier, the scientist who led the expedition which discovered and collected the holotype (original specimen) PULR-076. Zupaysaurus was first described and named in the scientific journal Ameghiniana by Argentine paleontologists Andrea Arcucci and Rodolfo Coria in 2003.