| Match | Date | Team | Score | Team | Venue | Attendance |
|---|
| 1 | 2016.02.28 | Thespakusatsu Gunma | 4-0 | FC Gifu | Shoda Shoyu Stadium Gunma | 8,418 |
| 2 | 2016.03.06 | FC Gifu | 0-4 | Hokkaido Consadole Sapporo | Gifu Nagaragawa Stadium | 4,898 |
| 3 | 2016.03.13 | FC Gifu | 1-0 | Giravanz Kitakyushu | Gifu Nagaragawa Stadium | 3,215 |
| 4 | 2016.03.20 | Ehime FC | 0-3 | FC Gifu | Ningineer Stadium | 3,549 |
| 5 | 2016.03.26 | FC Gifu | 1-0 | Mito HollyHock | Gifu Nagaragawa Stadium | 4,484 |
| 6 | 2016.04.03 | Tokushima Vortis | 1-3 | FC Gifu | Pocarisweat Stadium | 3,508 |
| 7 | 2016.04.09 | Kamatamare Sanuki | 3-2 | FC Gifu | Pikara Stadium | 2,350 |
| 8 | 2016.04.17 | FC Gifu | 0-2 | Matsumoto Yamaga FC | Gifu Nagaragawa Stadium | 6,295 |
| 9 | 2016.04.23 | Zweigen Kanazawa | 1-2 | FC Gifu | Ishikawa Athletics Stadium | 3,008 |
| 10 | 2016.04.29 | FC Gifu | 1-2 | Renofa Yamaguchi FC | Gifu Nagaragawa Stadium | 6,058 |
| 11 | 2016.05.03 | FC Machida Zelvia | 1-1 | FC Gifu | Machida Stadium | 6,034 |
| 12 | 2016.05.08 | FC Gifu | 1-1 | Shimizu S-Pulse | Gifu Nagaragawa Stadium | 6,124 |
| 13 | 2016.05.15 | Fagiano Okayama | 0-1 | FC Gifu | City Light Stadium | 9,464 |
| 14 | 2016.05.22 | JEF United Chiba | 3-2 | FC Gifu | Fukuda Denshi Arena | 10,147 |
| 15 | 2016.05.28 | FC Gifu | 0-1 | Montedio Yamagata | Gifu Nagaragawa Stadium | 8,248 |
| 16 | 2016.06.04 | FC Gifu | 2-4 | V-Varen Nagasaki | Gifu Nagaragawa Stadium | 4,074 |
| 17 | 2016.06.08 | Tokyo Verdy | 1-1 | FC Gifu | Ajinomoto Field Nishigaoka | 3,120 |
| 18 | 2016.06.12 | FC Gifu | 0-1 | Cerezo Osaka | Gifu Nagaragawa Stadium | 8,087 |
| 19 | 2016.06.19 | Yokohama FC | 1-2 | FC Gifu | NHK Spring Mitsuzawa Football Stadium | 3,017 |
| 20 | 2016.06.26 | FC Gifu | 2-3 | Roasso Kumamoto | Gifu Nagaragawa Stadium | 4,507 |
| 21 | 2016.07.03 | FC Gifu | 0-1 | Kyoto Sanga FC | Gifu Nagaragawa Stadium | 4,126 |
| 22 | 2016.07.10 | V-Varen Nagasaki | 2-1 | FC Gifu | Nagasaki Stadium | 7,901 |
| 23 | 2016.07.16 | Mito HollyHock | 1-0 | FC Gifu | K's denki Stadium Mito | 4,318 |
| 24 | 2016.07.20 | FC Gifu | 0-1 | Zweigen Kanazawa | Gifu Nagaragawa Stadium | 4,081 |
| 25 | 2016.07.25 | Hokkaido Consadole Sapporo | 5-0 | FC Gifu | Sapporo Dome | 11,301 |
| 26 | 2016.07.31 | Shimizu S-Pulse | 2-0 | FC Gifu | IAI Stadium Nihondaira | 11,143 |
| 27 | 2016.08.07 | FC Gifu | 1-1 | Kamatamare Sanuki | Gifu Nagaragawa Stadium | 4,431 |
| 28 | 2016.08.11 | Matsumoto Yamaga FC | 1-1 | FC Gifu | Matsumotodaira Park Stadium | 15,602 |
| 29 | 2016.08.14 | FC Gifu | 1-1 | Tokushima Vortis | Gifu Nagaragawa Stadium | 4,109 |
| 30 | 2016.08.21 | Montedio Yamagata | 1-1 | FC Gifu | ND Soft Stadium Yamagata | 6,005 |
| 31 | 2016.09.11 | FC Gifu | 0-2 | JEF United Chiba | Gifu Nagaragawa Stadium | 7,562 |
| 32 | 2016.09.18 | FC Gifu | 2-1 | Ehime FC | Gifu Nagaragawa Stadium | 3,549 |
| 33 | 2016.09.25 | Renofa Yamaguchi FC | 2-3 | FC Gifu | Ishin Memorial Park Stadium | 5,026 |
| 34 | 2016.10.02 | FC Gifu | 0-5 | Fagiano Okayama | Gifu Nagaragawa Stadium | 5,250 |
| 35 | 2016.10.08 | Cerezo Osaka | 3-2 | FC Gifu | Kincho Stadium | 9,391 |
| 36 | 2016.10.16 | Kyoto Sanga FC | 1-0 | FC Gifu | Kyoto Nishikyogoku Athletic Stadium | 7,299 |
| 37 | 2016.10.22 | FC Gifu | 1-2 | FC Machida Zelvia | Gifu Nagaragawa Stadium | 4,674 |
| 38 | 2016.10.30 | Giravanz Kitakyushu | 2-1 | FC Gifu | Honjo Stadium | 3,700 |
| 39 | 2016.11.03 | FC Gifu | 2-1 | Thespakusatsu Gunma | Gifu Nagaragawa Stadium | 3,920 |
| 40 | 2016.11.06 | FC Gifu | 2-0 | Yokohama FC | Gifu Nagaragawa Stadium | 9,060 |
| 41 | 2016.11.12 | Roasso Kumamoto | 1-0 | FC Gifu | Umakana-Yokana Stadium | 6,306 |
| 42 | 2016.11.20 | FC Gifu | 4-2 | Tokyo Verdy | Gifu Nagaragawa Stadium | 12,158 | |
Ruy Ramos