The 2016 Shimadzu All Japan Indoor Tennis Championships was a professional tennis tournament played on carpet. It was the 20th edition of the tournament which was part of the 2016 ATP Challenger Tour. It took place in Kyoto, Japan between 22 and 28 February.
| Country | Player | Rank1 | Seed | |
|---|---|---|---|---|
 Japan | Yūichi Sugita | 117 | 1 | |
| Japan | Tatsuma Ito | 120 | 2 | |
| Japan | Go Soeda | 131 | 3 | |
 Australia | Luke Saville | 184 | 4 | |
| Japan | Hiroki Moriya | 190 | 5 | |
 China | Bai Yan | 211 | 6 | |
| Chen Ti | 220 | 7 | ||
 Korea, Republic of | Lee Duck-hee | 230 | 8 |
The following players received wildcards into the singles main draw:
Sora Fukuda Shintaro Imai Ken Onishi Yasutaka UchiyamaThe following players received entry from the qualifying draw:
Andriej Kapaś Yuya Kibi Luke Saville Shuichi SekiguchiSee main article: article and 2016 Shimadzu All Japan Indoor Tennis Championships – Singles.
Yūichi Sugita def. Zhang Ze 5–7, 6–3, 6–4See main article: article and 2016 Shimadzu All Japan Indoor Tennis Championships – Doubles.
Gong Maoxin / Yi Chu-huan def. Go Soeda / Yasutaka Uchiyama 6–3, 7–6(9–7)