The sexes are slightly dimorphic in size, the males averaging larger than the females. A male weighing 78 g, and a female weighing 60 g were reported by Klingener, Genoways, and Baker (1978). Head and body length is 98 to 132 mm, and forearm length measures 70 to 92 mm.
The sexes are also dimorphic in color, with males having reddish to orange pelage dorsally, and females generally having greyish or dull brown fur. Both males and females tend to have paler underparts, and the pelage is extremely short.
Noctilionids have a pointed muzzle and lack a nose leaf. The nose is somewhat tubular and projects slightly beyond the lips. Upper lips are smooth but divided by a "hare lip", a vertical fold of skin under the nostrils. The lips are also large and swollen in appearance, suggesting the common name, greater bulldog bat.
This bat presents a formidable dentition. Its cheeks are elastic and can be greatly expanded. Internal cheek pouches are present. The ears are large, slender, pointed, and separate. There is also a tragus which has a serrated margin.
Noctilio leporinus has wings which are long and quite narrow, being more than two and a half times the length of the head and body. Nearly 65% of the wingspan is composed of the third digit.
The tail is more than half as long as the thigh bone. It extends to about the middle of a well-developed uropatagium, or tail membrane. The tail tip is free, protruding for about 10 to 15 mm from the dorsal surface of this membrane. The uropatagium is supported by the legs, tail, and calcar, or heel extension. The calcar is a cartilaginous structure that articulates with the heel bone (calcaneum) and is unique to bats. In this fishing species, the calcar is large and serves to hold the uropatagium out of the water as the bat flies close to the surface.
Noctilio leporinus has unusually long hind limbs and very large hind feet with strong gaff-like claws. Fishing bats tend to have hind feet 1.8 to 3.9 times larger than related non-fishing bats.