Fossils of Zapsalis were first described by American paleontologist Edward Drinker Cope in 1876 but as species of the large carnivorous theropod Laelaps (now Dryptosaurus).

[3][4][2] Cope named Zapsalis during the Bone Wars, his competition with Yale paleontologist Othniel Charles Marsh, to collect and describe as many fossil taxa as possible.

[5] After the Bone Wars, the type fossils of Zapsalis and the Laelaps species were sold to the American Museum of Natural History in New York.

[12] In 2013 Derek Larson and Philip Currie recognised Zapsalis as a valid taxon from the Judith River and Dinosaur Park Formation.

[13] In 2019, Currie and Evans announced that the Zapsalis teeth from the Dinosaur Park Formation represented the second premaxillary tooth of Saurornitholestes langstoni, in a paper describing a complete skull of that species.

[3][2] Currie & Evans, 2019 diagnosed Zapsalis from Saurornitholestes by noting the type of the former is lacking mesial serrations and being concave apicodistally, and therefore "recommended that the two genera be kept separate.