The country qualified athletes in cycling, goalball, judo, sailing, and wheelchair basketball.

Despite this, Tokyo will be the host city of the 2020 Summer Paralympics, a Japanese segment was performed during the closing ceremony.

[5] With one pathway for qualification being one highest ranked NPCs on the UCI Para-Cycling male and female Nations Ranking Lists on 31 December 2014, Japan qualified for the 2016 Summer Paralympics in Rio, assuming they continued to meet all other eligibility requirements.

[22] Semifinals Bronze Medal Match Shingo Kunieda represented Japan in wheelchair tennis.

[23] Shingo Kunieda, Takuya Miki, Satoshi Saida, Takashi Sanada all qualified in the men's singles event via the standard qualification route.

Kanako Domori, Yui Kamiji and Miho Nijo all qualified via the standard qualification route.