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
JPN	Yūichi Sugita	117	1
JPN	Tatsuma Ito	120	2
JPN	Go Soeda	131	3
AUS	Luke Saville	184	4
JPN	Hiroki Moriya	190	5
CHN	Bai Yan	211	6
TPE	Chen Ti	220	7
KOR	Lee Duck-hee	230	8

• ¹ Rankings are as of February 15, 2016.

The following players received wildcards into the singles main draw:

• Sora Fukuda
• Shintaro Imai
• Ken Onishi
• Yasutaka Uchiyama

The following players received entry from the qualifying draw:

• Andriej Kapaś
• Yuya Kibi
• Luke Saville
• Shuichi Sekiguchi

• Yūichi Sugita def. Zhang Ze 5–7, 6–3, 6–4

• Gong Maoxin / Yi Chu-huan def. Go Soeda / Yasutaka Uchiyama 6–3, 7–6^(9–7)

• Combined Main Draw