It is known from the holotype TMP 1983.25.1, a partial skull including the parietal and from the paratypes TMP 1999.55.292, isolated lateral ramus of right parietal and NMC 8803, central bar and lateral rami of parietals. AMNH 5656, AMNH 5401, NMC 1254, NMC 34832 and TMP 1979.11.147 were also referred to the genus. All specimens of Mojoceratops were collected from the Dinosaur Park Formation (late Campanian, 76.5–75 ma) of the Belly River Group of Alberta and Saskatchewan, western Canada. Mojoceratops was first named by Nicholas R. Longrich in 2010 and the type species is Mojoceratops perifania. It is based on fossils long thought to have belonged to Chasmosaurus.
The species Chasmosaurus kaiseni, known from a nearly complete (but partially restored) skull on display at the American Museum of Natural History, shares features in common with Mojoceratops perifania and may represent the same species. However, the parietal (back margin of the frill) is not preserved, and was restored in plaster based on other Chasmosaurus specimens, which caused confusion among scientists in previous decades. Because the parietal bone is critical for determining differences between species in ceratopsids like Chasmosaurus and Mojoceratops, C. kaiseni is regarded as a nomen dubium, rather than as the senior synonym of M. perifania.
The following cladogram shows the phylogeny of Chasmosaurinae according to a study by Scott Sampson e.a. in 2010.