The teens were in line to order at around 8:30pm on Saturday when the attacker reportedly entered the restaurant in the city of Kitakyushu and wordlessly stabbed them both.
Police have arrested a man in his 40s who lives nearby, public broadcaster NHK and other media outlets said. Officers could not immediately confirm the reports to AFP.
Saaya Nakashima was stabbed in the abdomen and later confirmed dead at a hospital.
The boy, who was stabbed in the waist area and remains in hospital, was quoted as saying they were “stabbed by a complete stranger”.