| 1 | Yu Takenouchi (Jpn) Colba-Superano Ham | 1:03:12 |
| 2 | Kazuhiro Yamamoto (Jpn) Cannondale Champion System | 0:01:22 |
| 3 | Masanori Kosaka (Jpn) Suwako Racing Team | 0:01:53 |
| 4 | Atsushi Maruyama (Jpn) JP Sports Test Team Massa-Andex | 0:02:09 |
| 5 | Makoto Shimada (Jpn) Shimano Drinking | 0:03:23 |
| 6 | Yoshitaka Hama (Jpn) Snel Cyclocross Team | 0:03:43 |
| 7 | Hikaru Kosaka (Jpn) Utsunomiya Blitzen CX Team | 0:04:05 |
| 8 | Kyosuke Takei (Jpn) Team Forza! | 0:04:26 |
| 9 | Yoshimitsu Tsuji (Jpn) Team Zenko | 0:04:31 |
| 10 | Masayuki Goda (Jpn) cycleclub3UP | 0:04:35 |
| 11 | Takafumi Iizuka (Jpn) | 0:04:47 |
| 12 | Takashi Miyazawa (Jpn) Saxo-Tinkoff | 0:05:18 |
| 13 | Seigo Yamamoto (Jpn) Suwako Racing Team | 0:05:19 |
| 14 | Shinya Ikemoto (Jpn) Wako Kiki Author | 0:05:28 |
| 15 | Hiroaki Kaneko (Jpn) Suwako Racing Team | 0:05:48 |
| 16 | Shintaro Nakama (Jpn) Team Edco Cyclocross-Giro | 0:06:17 |
| 17 | Yudai Izawa (Jpn) IWAI Shokai RacingTeam | |
| 18 | Masahiro Watanabe (Jpn) | |
| 19 | Toshioa Kunii (Jpn) Mile Post Racing | |
| 20 | Shuntaro Yamakawa (Jpn) Team Chainring | |
| 21 | Yuichi Suzuki (Jpn) Rise-Ride | |
| 22 | Kodai Izawa (Jpn) IWAI Shokai RacingTeam | |
| 23 | Makoto Kawamura (Jpn) | |
| 24 | Kazuaki Shirota (Jpn) Snel Cyclocross Team | |
| 25 | Takashi Makino (Jpn) Cogs | |
| 26 | Obuchi Koki (Jpn) | |
| 27 | Tomohiro Saito (Jpn) Ridelife Gian | |
| 28 | Kazuyoshi Izawa (Jpn) Tonic CX Team Japan | |
| 29 | James Machin (GBr) Champion System | |
| 30 | Toyoshige Ikeyama (Jpn) Hunter Simworks CX Team | |
| 31 | Yukikaze Ishiyama (Jpn) Esquina Racing | |
| 32 | Ryoji Nemoto (Jpn) Champion System | |
| 33 | Masashi Matsui (Jpn) Shimano Drinking | |
| 34 | Shun Matsumoto (Jpn) Mashun MTB Racing | |
| 35 | Goro Akiyama (Jpn) Gruppo Acqua Tama | |
| 36 | Toi Yoshimizu (Jpn) IWAI Shokai RacingTeam | |
| 37 | Yuichi Sawada (Jpn) Team Cyclemind | |
| 38 | Jin Kanai (Jpn) Delapista | |
| 39 | Yuki Ochiai (Jpn) Hunter Simworks CX Team | |
| 40 | Koudai Takeda (Jpn) | |
| 41 | Koichi Matsumura (Jpn) Yatsugatake Cyclocross Club | |
| 42 | Manabu Nemoto (Jpn) | |
| 43 | Kunihiko Kaji (Jpn) Narushima Frend | |
| 44 | Yusuke Yamagishi (Jpn) Hunter Simworks CX Team | |
| 45 | Toshihide Sato (Jpn) Chainring CX Racing | |
| 46 | Yuki Ikeda (Jpn) Topeak Ergon Racing Team | |
| 47 | Katsuhisa Baba (Jpn) Jitensha no Mori | |
| 48 | Yoshiaki Shirota (Jpn) W.V.OTA.twin | |
| 49 | Hiroto Yamashita (Jpn) Team Youcan | |
| 50 | Masato Samata (Jpn) Wildboars | |
| 51 | Hirohide Kubota (Jpn) Yatsugatake Cyclocross Club | |
| 52 | Masanori Kuniyoshi (Jpn) Bridler | |
| 53 | Junichiro Hashiguchi (Jpn) | |
| 54 | Kodai Ichimori (Jpn) Team Tamagawa | |
| 56 | Satoshi Inagaki (Jpn) Team Maruichi | |
| 57 | Hiroyuki Ando (Jpn) Salata Bianca Kobe Esquina | |
| 55 | Toru Yokoyama (Jpn) Hadano Cyclocross Team | |
| 58 | Kenichiro Onishi (Jpn) IWAI Shokai RacingTeam | |
| 59 | Daigoro Kumamoto (Jpn) Yatsugatake Cyclocross Club | |
| 60 | Kenichi Il (Jpn) | |
| 61 | Yoshonori Suzuki (Jpn) Volca | |
| 62 | Wataru Hatanaka (Jpn) Yatsugatake Cyclocross Club | |
