Sakura Yosozumi, 19, won gold with a score of 60.09 on Wednesday.
After French rower Noel Vandernotte, Kokona Hiraki becomes the youngest Olympic medallist.
Kokona Hiraki finished with a score of 58.05. She wore a white boiler suit during the event.
She is Japan’s youngest summer Olympian, surpassing swimmer Yukari Takemoto.
Japan have secured five of the nine medals so far as skateboarding makes its Olympic debut.