Trilophosuchus is known from a posterior portion of the skull, QM F16856, the holotype specimen. Several other isolated bones of the skull were found. The material was collected from the Ringtail Site of the Gag Plateau in Riversleigh, one of Australia's most famous fossil localities. The skull was uncovered in 1985 during an excavation by the University of New South Wales. The deposit in which Trilophosuchus were found are Early Miocene in age, roughly 20 million years old. The deposit, known as System C, is the youngest of the Oligocene-Miocene sequences at Riversleigh. The genus Trilophosuchus was erected in 1993 with the description of the remains by Paul Willis of the University of Sydney in the Journal of Vertebrate Paleontology.