Honda began her season with a gold medal at the 2016 Asian Trophy. She was assigned to the JGP events in Japan and Slovenia. In her first event at JGP Yokohama, she placed fifth in the short program and won the free skate with a junior world record of 128.64 points to place second overall. In her next event at JGP Ljubljana, she won another silver medal, qualifying her for her second JGP Final. However, she withdrew from the Final, citing illness. In November, she won the bronze medal at the Japan Junior National Championships.