| No. | Site | Location | Year of Inscription | Category |
| 1 | Buddhist Monuments in the Horyu-ji Area | Nara | 1993 | Cultural |
| 2 | Himeji-jo | Hyogo | 1993 | Cultural |
| 3 | Yakushima | Kagoshima | 1993 | Natural |
| 4 | Shirakami-Sanchi | Aomori Akita |
1993 | Natural |
| 5 | Historic Monuments of Ancient Kyoto (Kyoto, Uji and Otsu Cities) | Kyoto Shiga |
1994 | Cultural |
| 6 | Historic Villages of Shirakawa-go and Gokayama | Gifu Toyama |
1995 | Cultural |
| 7 | Hiroshima Peace Memorial (Genbaku Dome) | Hiroshima | 1996 | Cultural |
| 8 | Itsukushima Shinto Shrine | Hiroshima | 1996 | Cultural |
| 9 | Historic Monuments of Ancient Nara | Nara | 1998 | Cultural |
| 10 | Shrines and Temples of Nikko | Tochigi | 1999 | Cultural |
| 11 | Gusuku Sites and Related Properties of the Kingdom of Ryukyu | Okinawa | 2000 | Cultural |
| 12 | Sacred Sites and Pilgrimage Routes in the Kii Mountain Range | Mie Nara Wakayama |
2004 | Cultural |
| 13 | Shiretoko | Hokkaido | 2005 | Natural |
| 14 | Iwami Ginzan Silver Mine and its Cultural Landscape | Shimane | 2007 | Cultural |
| 15 | Ogasawara Islands | Tokyo | 2011 | Natural |
| 16 | Hiraizumi – Temples, Gardens and Archaeological Sites Representing the Buddhist Pure Land | Iwate | 2011 | Cultural |
| 17 | Fujisan, Sacred Place and Source of Artistic Inspiration | Yamanashi Shizuoka |
2013 | Cultural |
| 18 | Tomioka Silk Mill and Related Sites | Gunma | 2014 | Cultural |
| 19 | Sites of Japan’s Meiji Industrial Revolution: Iron and Steel, Shipbuilding and Coal Mining | Fukuoka Saga Nagasaki Kumamoto Kagoshima Yamagushi Iwate Shizuoka |
2015 | Cultural |
| 20 | The Architectural Work of Le Corbusier, an Outstanding Contribution to the Modern Movement | Tokyo ※France, Germany, Switzerland, Belgium, Argentina, India |
2016 | Cultural |
| 21 | Sacred Island of Okinoshima and Associated Sites in the Munakata Region | Fukuoka | 2017 | Cultural |
| 22 | Hidden Christian Sites in the Nagasaki Region | Nagasaki Kumamoto |
2018 | Cultural |
| 23 | Mozu-Furuichi Kofun Group: Mounded Tombs of Ancient Japan | Osaka | 2019 | Cultural |
| 24 | Amami-Oshima Island, Tokunoshima Island, Northern part of Okinawa Island, and Iriomote Island | Kagoshima Okinawa |
2021 | Natural |
| 25 | Jomon Prehistoric Sites in Northern Japan | Hokkaido Aomori Iwate Akita |
2021 | Cultural |
