Calificación 250cc - Gran Premio de Japón 2009
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Marco Simoncelli |
Metis Gilera | Gilera | |
| 2 | 
Hiroshi Aoyama |
Scot Racing Team | Honda | +0.602 |
| 3 | 
Alvaro Bautista |
Mapfre Aspar Team | Aprilia | +0.743 |
| 4 |
Mattia Pasini |
Team Toth Aprilia | Aprilia | +0.847 |
| 5 |
Héctor Barberá |
Pepe World Team | Aprilia | +1.404 |
| 6 |
Raffaele De Rosa |
Scot Racing Team | Honda | +1.491 |
| 7 | 
Gabor Talmacsi |
Balaton Racing Team | Aprilia | +1.501 |
| 8 | 
Mike Di Meglio |
+1.502 | ||
| 9 |
Roberto Locatelli |
Metis Gilera | Gilera | +1.664 |
| 10 |
Alex Debón |
Aeropuerto-Castello-Blusens | Aprilia | +2.010 |
| 11 | 
Lukas Pesek |
Auto Kelly - CP | Aprilia | +2.065 |
| 12 | 
Ratthapark Wilairot |
Thai Honda PTT SAG | Honda | +2.115 |
| 13 | 
Thomas Lüthi |
Emmi - Caffe Latte | Aprilia | +2.360 |
| 14 |
Jules Cluzel |
Matteoni Racing | Aprilia | +2.445 |
| 15 |
Héctor Faubel |
Thai Honda PTT SAG | Honda | +2.495 |
| 16 |
Karel Abraham |
Cardion AB Motoracing | Aprilia | +2.631 |
| 17 |
Shuhei Aoyama |
Racing Team Germany | Honda | +2.836 |
| 18 |
Alex Baldolini |
WTR San Marino Team | Aprilia | +2.924 |
| 19 |
Kazuki Watanabe |
Bardral Racing | Yamaha | +4.181 |
| 20 |
Imre Toth |
Team Toth Aprilia | Aprilia | +5.634 |
| 21 |
Axel Pons |
Pepe World Team | Aprilia | +7.951 |
| 22 | 
Vladimir Leonov |
Viessmann Kiefer Racing | Aprilia | +8.354 |
| 23 |
Bastien Chesaux |
Racing Team Germany | Honda | +8.860 |
| 24 |
Aitor Rodríguez |
Milar - Juegos Lucky | Aprilia | +10.344 |
| 25 |
Shoya Tomizawa |
CIP Moto | Honda | +10.785 |