| Pos. | No. | Class | Rider | Type | Time | Delay | Gap | Lap | Team | ||||
| 1 | 42 | WT | Takahiro Yamamoto | Ninja250 | 2'17.883 | 125.36km/h | 3/7 | YSS Mercury & Santa | |||||
| 2 | 28 | WT | Katsu Mikami | ZZR250 | 2'19.596 | 1.713 | 1.713 | 5/7 | WIN RF | ||||
| 3 | 27 | ST-R25 | Hiroshi Maruyama | YZF-R25 | 2'20.241 | 2.358 | 0.645 | 7/7 | WITH ME RACING | ||||
| 4 | 65 | ST-R25 | Hiroki Uehara | YZF-R25 | 2'20.274 | 2.391 | 0.033 | 6/7 | SP Tadao Racing Team | ||||
| 5 | 53 | ST-R25 | Takeda Makoto | YZF-R25 | 2'20.403 | 2.520 | 0.129 | 7/7 | Motoreacing & Akigase | ||||
| 6 | 3 | WT | Takahito Ueda | Ninja250 | 2'20.706 | 2.823 | 0.303 | 6/7 | RS−ITOH | ||||
| 7 | 14 | WT | Toshio Higashiura | YZF-R25 | 2'21.249 | 3.366 | 0.543 | 6/6 | YSP Nishi Tokyo with PLUS μ | ||||
| 8 | 9 | WT | Kenji Fujio | YZF-R25 | 2'21.508 | 3.625 | 0.259 | 7/7 | Plasmu Racing & NA Association A Team | ||||
| 9 | 51 | ST-R25 | Tetsuya Usui | YZF-R25 | 2'21.565 | 3.682 | 0.057 | 7/7 | 51 Garage Team Iwaki | ||||
| 10 | 6 | Brave | Hirokazu Taura | PPD5 | 2'22.431 | 4.548 | 0.866 | 2/2 | Pew Pew Electric | ||||
| 11 | 54 | WT | Yasuhiko Negishi | Ninja250R | 2'22.760 | 4.877 | 0.329 | 6/7 | Presto MRC Old Man's Struggle | ||||
| 12 | 74 | ST-R25 | Tetsu Tokita | YZF-R25 | 2'23.747 | 5.864 | 0.987 | 6/6 | Motorcycle Japan No.1 | ||||
| 13 | 822 | WT | Sato Kimikazu | Ninja250R | 2'24.714 | 6.831 | 0.967 | 6/7 | Senna's High-Speed Run + KS Dental | ||||
| 14 | 30 | ST-Ninja | Mori Daisaku | Ninja250R | 2'25.085 | 7.202 | 0.371 | 6/6 | Kiriga Racing | ||||
| 15 | 810 | ST-Ninja | Atsushi Shiratori | Ninja250R | 2'25.097 | 7.214 | 0.012 | 3/6 | 8810R | ||||
| 16 | 71 | WT | Hiroshi Otsuki | YZF-R25 | 2'25.141 | 7.258 | 0.044 | 6/6 | Plasmu Racing & NA Association B Team | ||||
| 17 | 61 | ST-Ninja | Satoshi Sekiguchi | Ninja250R | 2'25.659 | 7.776 | 0.518 | 6/6 | Auto Boy J's & Yoshinari Matsushita #61 | ||||
| 18 | 90 | WS | Takata Higashi | TZX3.2R | 2'25.670 | 7.787 | 0.011 | 6/6 | Alright! Meeting is fine. | ||||
| 19 | 39 | WT | Sato Gaku | YZF-R25 | 2'25.819 | 7.936 | 0.149 | 4/6 | Onoe Service | ||||
| 20 | 111 | WT | Kikuchihara Takashi | SP3 Cart MC20 | 2'26.254 | 8.371 | 0.435 | 6/6 | Madoka Design & SP3 & Affini | ||||
| 21 | 114 | ST-R25 | Kazuo Watanabe | YZF-R25 | 2'26.265 | 8.382 | 0.011 | 6/6 | Just going to Motegi will give you 10 Mote endurance | ||||
| 22 | 102 | WT | Katsuhito Ogawa | Ninja250 | 2'26.384 | 8.501 | 0.119 | 6/6 | Rider's Club RT | ||||
| 23 | 62 | WT | Motegi Daichi | YZF-R25 | 2'26.390 | 8.507 | 0.006 | 6/6 | CLUB MASSA-R | ||||
| 24 | 45 | WT | Kubota Akinori | VT250 SPADA | 2'26.431 | 8.548 | 0.041 | 5/6 | RT Kinnoji | ||||
| 25 | 117 | WT | Yoji Okubo | GPZ250R | 2'26.645 | 8.762 | 0.214 | 6/6 | Y-style | ||||
| 26 | 82 | ST-Ninja | Koji Kikuchi | Ninja250R | 2'26.871 | 8.988 | 0.226 | 5/6 | Kito Kito RT Najirane | ||||
| 27 | 85 | WT | Hideki Ito | NINJA250R Modified | 2'27.193 | 9.310 | 0.322 | 2/4 | TEAM Success & KTS Shonan | ||||
| 28 | 106 | ST-Ninja | Hiroshi Igawa | Ninja250R | 2'27.374 | 9.491 | 0.181 | 6/6 | Team Kana | ||||
| 29 | 76 | WT | Kameya Masato | VT250 SPADA | 2'27.505 | 9.622 | 0.131 | 6/6 | Team Galinco U | ||||
| 30 | 94 | ST-Ninja | Suzuki Gorou | Ninja250 | 2'27.622 | 9.739 | 0.117 | 6/6 | Gripper | ||||
| 31 | 109 | WT | Satoshi Hazeta | VTR250 | 2'28.075 | 10.192 | 0.453 | 5/6 | The color of men is purple. | ||||
| 32 | 48 | ST-Ninja | Hashimoto Minoru | Ninja250 | 2'28.445 | 10.562 | 0.370 | 5/6 | YDS☆RSK☆NEXZAS | ||||
| 33 | 20 | WT | Fujisawa Akira | YZF-R25 | 2'28.482 | 10.599 | 0.037 | 6/6 | TEAM-ARS and T.T.moto | ||||
| 34 | 118 | WS | Kaishiro Watanabe | RC250 | 2'28.485 | 10.602 | 0.003 | 5/6 | Bikers S Clararacing & KTM | ||||
| 35 | 34 | ST-Ninja | Shigeo Kuwabara | Ninja250R | 2'28.921 | 11.038 | 0.436 | 5/6 | SEEKS and G!trax | ||||
| 36 | 150 | ST-R25 | Yusuke Fukasawa | YZF-R25 | 2'28.989 | 11.106 | 0.068 | 6/6 | YF DESIGN & RT Fifty Steps Hundred Steps | ||||
| 37 | 67 | WS | Hiromitsu Takemura | RC250 | 2'30.367 | 12.484 | 1.378 | 3/5 | Riding Sports Fire B | ||||
| 38 | 16 | WT | Shota Inaba | VT250 | 2'30.485 | 12.602 | 0.118 | 5/5 | Meijiya Restaurant | ||||
| 39 | 49 | WT | Tatsuya Ishigaki | YZF-R25 | 2'31.481 | 13.598 | 0.996 | 5/6 | YSP Itabashi Central Racing Team | ||||
| 40 | 64 | WT | Matsuda Flat | VTZ | 2'42.882 | 24.999 | 11.401 | 4/4 | Kitokito RT Delaboree | ||||
| 41 | 55 | ST-VTR | Hideyoshi Sonobe | VTR250 | 2'45.553 | 27.670 | 2.671 | 5/6 | Troy Racing Team | ||||
| 105 | WT | Hirohiko Miyamoto | VTR250 | Did not participate | OutRun Rabbit Destroyer |