Calificación Moto3 Gran Premio de Malasia 2016
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Brad Binder |
Red Bull KTM Ajo | KTM | 2:26.268 |
| 2 | 
Jorge Navarro |
Estrella Galicia 0,0 | Honda | +0.093 |
| 3 | 
Francesco Bagnaia |
ASPAR Mahindra Team Moto3 | Mahindra | +0.127 |
| 4 |
Lorenzo Dalla Porta |
SKY Racing Team VR46 | KTM | +0.810 |
| 5 | 
Gabriel Rodrigo |
RBA Racing Team | KTM | +1.039 |
| 6 |
Niccolo Antonelli |
Ongetta-Rivacold | Honda | +1.087 |
| 7 | 
Bo Bendsneyder |
Red Bull KTM Ajo | KTM | +1.336 |
| 8 |
Adrián Martín |
MAPFRE Team MAHINDRA | Mahindra | +1.374 |
| 9 | 
Fabio Quartararo |
Leopard Racing | KTM | +1.393 |
| 10 |
Arón Canet |
Estrella Galicia 0,0 | Honda | +1.656 |
| 11 |
Andrea Locatelli |
Leopard Racing | KTM | +1.719 |
| 12 | 
Philipp Oettl |
Schedl GP Racing | KTM | +1.794 |
| 13 |
Nicolo Bulega |
SKY Racing Team VR46 | KTM | +1.801 |
| 14 |
Joan Mir |
Leopard Racing | KTM | +1.925 |
| 15 | 
Jakub Kornfeil |
Drive M7 SIC Racing Team | Honda | +1.947 |
| 16 | 
Tatsuki Suzuki |
CIP | Mahindra | +2.285 |
| 17 |
Juanfran Guevara |
RBA Racing Team | KTM | +2.450 |
| 18 | 
Adam Norrodin |
Drive M7 SIC Racing Team | Honda | +2.697 |
| 19 |
Fabio Di Giannantonio |
Gresini Racing Moto3 | Honda | +2.714 |
| 20 |
Khairul Idham Pawi |
Honda Team Asia | Honda | +2.721 |
| 21 | 
Alex Fabbri |
+2.999 | ||
| 22 |
Hafiq Azmi |
Peugeot MC Saxoprint | Peugeot | +3.066 |
| 23 | 
Livio Loi |
RW Racing GP BV | Honda | +3.112 |
| 24 |
Jules Danilo |
Ongetta-Rivacold | Honda | +3.327 |
| 25 |
Hiroki Ono |
Honda Team Asia | Honda | +3.980 |
| 26 |
Andrea Migno |
SKY Racing Team VR46 | KTM | +4.479 |
| 27 |
Albert Arenas |
Peugeot MC Saxo | Albert Arenas | +4.604 |
| 28 |
Marcos Ramírez |
Platinum Bay Real Estate | Mahindra | +4.693 |
| 29 |
Lorenzo Petrarca |
3570 Team Italia | Stefano Valtulini | +5.883 |
| 30 |
Stefano Valtulini |
3570 Team Italia | Stefano Valtulini | +6.078 |
| 31 |
Darryn Binder |
Platinum Bay Real Estate | Mahindra | +6.324 |
| 32 |
María Herrera |
Team Laglisse | Honda | +10.430 |
| 33 |
Fabio Spiranelli |
CIP | Mahindra | +0.000 |