The holotype specimen, SFM-0001, was excavated from the Bessho Formation in the Nagano Prefecture in Japan in 1988 by the residents of Shiga-mura with assistance from the staff of the Shiga Fossil Museum.

[1] The specimen is nearly complete, and consists of a partial skull, the jawbone, the lingual bone in the neck, vertebrae, ribs, the breastbone, and humeri and radii in the limbs.

[1][2] It was dated to the Langhian stage of the Miocene 14–15 million years ago (mya), and the specimen is currently on display at the Gunma Museum of Natural History in Japan.

[5] Like other raptorials, Brygmophyseter had enamel-coated teeth in both jaws, unlike the modern sperm whale (Physeter macrocephalus).

The ulna was more primitive than that of the modern sperm whale, in that the shaft was longer and more slender, and the head of the bone was smaller.

[1] Brygmophyseter is a member of a fossil stem group of hyper-predatory macroraptorial sperm whales from the Miocene (often shortened to "raptorial").

The other members are Acrophyseter, Albicetus, Livyatan, and Zygophyseter, and these five whales have in common enamel-coated teeth in both the upper and lower jaws which were used in hunting large prey.

[9] It has been proposed that these raptorials be placed into the extinct paraphyletic (hence, probably invalid) subfamily Hoplocetinae, alongside Scaldicetus, Diaphorocetus, Idiorophus, and Hoplocetus.

Therefore, the study authored by paleontologists Kimura Toshiyuki, Hasegawa Yoshikazu, and Barnes Lawrence placed it into the newly erected genus Brygmophyseter.

Though no stomach remains or bite marks have been found, it is thought to have preyed upon a variety of animals, including whales, seals, fish, and cephalopods.

[18] Brygmophyseter was featured in the fifth episode of The History Channel's Jurassic Fight Club, "Deep Sea Killers".