Fossils of this animal have been found in southern Germany and dated from the Ladinian stage of the Middle Triassic period, around 242 to 237 million years ago.

The locality where Batrachotomus lived was a swampy region and the name comes from the Greek batrachos/βάτραχος (frog) and tome/τομή (cutting, slicing), which refers to its preying on the large amphibian Mastodonsaurus.

[8] As a typical archosaur, Batrachotomus had two antorbital fenestrae between the orbits and nostrils, and a fifth pair of small openings at the rear part of the lower jaw.

Fossil collector Johann G. Wegele discovered the first specimens in a 1977 excavation at the Erfurt Formation, dated from the Longobardian (late Ladinian) age.

[7][12] In 1999, palaeontologist David J. Gower described the holotype (SMNS 52970) from the 1977 excavation, which is the largest specimen of the genus,[12][13] comprised by incomplete skull and postcranial material.

[14][18] Sterling J. Nesbitt (2011) revised the classification of basal archosaurs, and using the most comprehensive phylogenetic analysis for this group (to date) found Prestosuchidae to be non-monophyletic.

[20][21] In a yet to be formally published revision of Heptasuchus, a medium/large-sized (~6.5 m long) "rauisuchian" from the upper Chugwater Group of Wyoming, it was recovered as the sister taxon of Batrachotomus using a derivative of Nesbitt (2011) analysis.

[22] The cladogram below follows an analysis by Sterling J. Nesbitt (2011):[23] Avemetatarsalia Ornithosuchidae Gracilisuchus Turfanosuchus Revueltosaurus Aetosauria Ticinosuchus Poposauroidea Prestosuchus Saurosuchus Batrachotomus Fasolasuchus Rauisuchus Polonosuchus Postosuchus Crocodylomorpha Since 1977, the rich vertebrate fauna found at Baden-Württemberg reflects a moist region of the Middle Triassic in Germany.

Along with Batrachotomus, palaeontologists recovered remains of fishes, amphibians, such as Gerrothorax and Mastodonsaurus, and even animals like nothosaurs and the distinct marine reptile Tanystropheus.