We describe a new crocodile, Crocodylus thorbjarnarsoni, sp. nov., on the basis of skulls and jaws from Pliocene and Pleistocene deposits in the Lake Turkana Basin of Kenya. The new species has a comparatively broad, deep snout and resembles an extinct horned crocodile from the Quaternary of Olduvai Gorge (C. anthropophagus), but the squamosal ‘horns’ are not as well developed. The skull table has a strongly trapezoidal outline different from those of the living Nile crocodile (C. niloticus) and crocodiles from late Miocene deposits in the Turkana Basin. The largest specimens are from animals up to 7.5 m in total length. It would have been the largest predator in its environment, and the early humans found in the same deposits were presumably part of its prey base. A phylogenetic analysis, including the new species and an improved sample of extinct crocodyline diversity, suggests a more complex phylogenetic and biogeographic history for the clade in Africa and the eastern Indian Ocean region than previously supposed. The analysis limits the known geographic and stratigraphic range of Rimasuchus lloydi, previously thought to occur throughout Africa from the early Miocene through the Pleistocene of northern Africa. Crocodylus niloticus is not known with certainty from units older than the Quaternary, and most late Miocene fossils from the Turkana Basin previously referred to C. niloticus can instead be referred to C. checchiai. The current first appearance datum for Crocodylus in Africa is approximately 7 Ma.