2013/08/31 | Naruto Tokushima | | 0-2 | | Saga University | | | | |
| Hokkaido University | | 2-1 | | Haguro High School | | | | |
| Yamanashi Gakuin University | | 1-2 | | Fukushima United | | | | |
| Mind House Yokkaichi | | 0-1 | | Niigata University | | | | |
| Tochigi Uva | | 2-1 | | Tokyo Int. University | | | | |
| Kamatamare Sanuki | | 7-2 | | Takamatsu High School | | | | |
| Fukui United | | 1-0 | | Miyazaki Sangyo-keiei University | | | | |
| Ryukyu | | 2-1 Pro. | | Dezzolla Shimane | | | | |
| Nagano Parceiro | | 4-1 | | Toyota Shukyudan | | | | |
| Sagawa Printing SC | | 2-0 | | MIO Biwako Shiga | | | | |
| University of Tsukuba | | 4-1 Pro. | | Urayasu SC | | | | |
2013/09/01 | Kumagaku High School | | 1-9 | | Imabari | | | | |
| Grulla Morioka | | 0-1 | | Sony Sendai | | | | |
| Arterivo Wakayama | | 2-3 Pro. | | Fujieda MYFC | | | | |
| Zweigen Kanazawa | | 6-1 | | Toyama Shinjo | | | | |
| Kanoya Taiiku University | | 0-1 | | Kochi University | | | | |
| Vanraure Hachinohe | | 1-0 | | Toin University | | | | |
| Yonago Kita High School | | 0-2 | | Fagiano Okayama B | | | | |
| Nara | | 3-2 Pro. | | Kwansei Gakuin University | | | | |
| Gifu B | | 1-2 | | Kansai University | | | | |
| Thespa Kusatsu B | | 0-3 Pro. | | Yokogawa Musashino | | | | |
| Blaublitz Akita | | 2-0 | | Renofa Yamaguchi | | | | |
| Sagawa Express | | 1-4 | | Fukuoka University | | | | |
| Heavy Industrial | | 1-2 | | Hoyo Oita | | | | |