Calificación Moto3 - Gran Premio de Italia 2016
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Romano Fenati |
SKY Racing Team VR46 | KTM | 1:57.289 |
| 2 |
Andrea Migno |
SKY Racing Team VR46 | KTM | +0.297 |
| 3 | 
Khairul Idham Pawi |
Honda Team Asia | Honda | +0.316 |
| 4 | 
Brad Binder |
Red Bull KTM Ajo | KTM | +0.372 |
| 5 | 
Jorge Navarro |
Estrella Galicia 0,0 | Honda | +0.667 |
| 6 |
Enea Bastianini |
Gresini Racing Moto3 | Honda | +0.705 |
| 7 |
Nicolo Bulega |
SKY Racing Team VR46 | KTM | +0.724 |
| 8 |
Francesco Bagnaia |
ASPAR Mahindra Team Moto3 | Mahindra | +0.760 |
| 9 |
Arón Canet |
Estrella Galicia 0,0 | Honda | +0.834 |
| 10 |
Joan Mir |
Leopard Racing | KTM | +0.862 |
| 11 | 
Hiroki Ono |
Honda Team Asia | Honda | +0.863 |
| 12 |
Fabio Di Giannantonio |
Gresini Racing Moto3 | Honda | +0.939 |
| 13 | 
Bo Bendsneyder |
Red Bull KTM Ajo | KTM | +1.016 |
| 14 |
Lorenzo Dalla Porta |
SKY Racing Team VR46 | KTM | +1.054 |
| 15 |
Adrián Martín |
MAPFRE Team MAHINDRA | Mahindra | +1.055 |
| 16 | 
Jakub Kornfeil |
Drive M7 SIC Racing Team | Honda | +1.086 |
| 17 |
Andrea Locatelli |
Leopard Racing | KTM | +1.137 |
| 18 | 
Fabio Quartararo |
Leopard Racing | KTM | +1.197 |
| 19 |
Karel Hanika |
Platinum Bay Real Estate | Mahindra | +1.205 |
| 20 |
Tatsuki Suzuki |
CIP | Mahindra | +1.231 |
| 21 | 
Gabriel Rodrigo |
RBA Racing Team | KTM | +1.288 |
| 22 |
Niccolo Antonelli |
Ongetta-Rivacold | Honda | +1.317 |
| 23 | 
Livio Loi |
RW Racing GP BV | Honda | +1.387 |
| 24 |
Darryn Binder |
Platinum Bay Real Estate | Mahindra | +1.456 |
| 25 |
Jules Danilo |
Ongetta-Rivacold | Honda | +1.474 |
| 26 |
Juanfran Guevara |
RBA Racing Team | KTM | +1.478 |
| 27 |
Alexis Masbou |
Peugeot MC Saxo | Albert Arenas | +1.642 |
| 28 | 
John Mcphee |
SaxoPrint RTG | Peugeot | +1.752 |
| 29 |
María Herrera |
Team Laglisse | Honda | +1.971 |
| 30 |
Stefano Valtulini |
3570 Team Italia | Stefano Valtulini | +2.159 |
| 31 |
Adam Norrodin |
Drive M7 SIC Racing Team | Honda | +2.164 |
| 32 |
Fabio Spiranelli |
CIP | Mahindra | +3.193 |
| 33 |
Lorenzo Petrarca |
3570 Team Italia | Stefano Valtulini | +3.281 |