Officials from the Tokyo Sea Life Park discovered the 4.3-foot-long (1.3-meter-long) creature on January 25 during an expedition with local fishermen. The shark had been tangled in fishing nets 500 to 650 feet (150 to 200 meters) deep.
But the animal died on the morning of January 27 after being put on display for the public.
Little is known about the mysterious goblin shark, which normally stays near the bottom of the ocean.
"Dead goblin sharks are caught from time to time, but it is rarely seen alive," a park official told the AFP news agency. "We were able to document the way the shark swims. After it died, we dissected the specimen for further studies."
But the unusual find is giving scientists déjà vu.
Earlier this month another deep-sea prehistoric shark had been found in Japan—a frilled shark spotted on January 21 that, like the goblin, died quickly in captivity.