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. In contrast with sprawling reptiles, like crocodiles, this large carnivore was very agile with locomotor superiority due to its erect stance. A remarkable feature seen on its back was a row of paired, flattened bony plates. Batrachotomus was possibly an early relative of Postosuchus, which lived during the dawn of the dinosaurs.
Batrachotomus was a heavily built, large quadrupedal reptile reaching 6 metres (20 ft) in length. A trait that characterized Batrachotomus, compared to other crurotarsans, was a series of paired small plates on its back which were attached to each vertebra. These bony deposits forming scales are called osteoderms. Flattened and leaf-shaped, these extended from behind the head along the column and reducing in size, ended at the tail. There is also evidence that osteoderms were present on the ventral region of the tail, as seen in Ticinosuchus ferox, and even on the flank, belly and limbs.
Like rauisuchians, Batrachotomus walked with an erect posture, although the limbs were not located directly under the trunk. The limbs were not equal in length as the forelimbs were about 70% of the hindlimbs. The toe bones (phalanges) are poorly preserved and the only well known bone is a fifth metatarsal (bone in hindlimbs attached to the toe bones) which was hooked in shape. However, hypotheses suggest that probably each forelimb had four toes and each hindlimb five.
Batrachotomus had a tall and narrow skull estimated at 40 to 50 cm (1.3 to 1.6 ft) in length. It had five pairs of fenestrae (skull openings), two pairs of which were for the eyes (called orbits) and the nostrils. Behind the orbits were two temporal fenestrae. These holes probably helped to reduce the weight of the skull and enabled the jaw to open more widely. 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.
The jaws contained sharp teeth which were compressed laterally and unequal in size and shape, and this variation of tooth shape is known as heterodonty. The teeth on the premaxillae (bones at the very tip of the upper jaw) were slender, unlike those of the maxillae (the main tooth-bearing bones in the upper jaw) which had a straight posterior edge. The upper jaw bore 30 teeth, with each premaxilla carrying about 4 teeth and each maxilla 11, while the lower jaw held 22 teeth.