The teens were in line to order around 8:30 pm (1130 GMT) on Saturday when the attacker entered the fast-food restaurant and wordlessly stabbed them both, according to national broadcaster NHK.
It was not clear whether the girl knew the man, who remained at large on Sunday.
Police declined to comment on the case to AFP.
Violent crime is rare in Japan, which has strict gun control laws. But there are occasional stabbings and even shootings, including the assassination of former prime minister Shinzo Abe in 2022.
The 51-year-old attacker slashed at a group of children before fatally stabbing himself.
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