Kanaya had a successful amateur career, winning the 2015 Japan Amateur Championship and the 2018 Asia-Pacific Amateur Championship. The latter gave him entry to the Masters and the Open Championship in 2019. He played in a number of representative matches, including the 2018 Eisenhower Trophy where he had the second best individual score. Kanaya won team gold medals at the 2017 Summer Universiade and at the 2018 Asian Games. He was world ranked number 1 in the World Amateur Golf Ranking for 55 weeks, winning the Mark H. McCormack Medal for 2020.