Calificación Moto3 - Gran Premio de San Marino 2016
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Brad Binder |
Red Bull KTM Ajo | KTM | 1:42.398 |
| 2 | 
Enea Bastianini |
Gresini Racing Moto3 | Honda | +0.150 |
| 3 |
Nicolo Bulega |
SKY Racing Team VR46 | KTM | +0.233 |
| 4 | 
Jakub Kornfeil |
Drive M7 SIC Racing Team | Honda | +0.261 |
| 5 | 
Jorge Navarro |
Estrella Galicia 0,0 | Honda | +0.312 |
| 6 |
Arón Canet |
Estrella Galicia 0,0 | Honda | +0.444 |
| 7 | 
Philipp Oettl |
Schedl GP Racing | KTM | +0.557 |
| 8 | 
Hiroki Ono |
Honda Team Asia | Honda | +0.564 |
| 9 |
Juanfran Guevara |
RBA Racing Team | KTM | +0.587 |
| 10 |
Fabio Di Giannantonio |
Gresini Racing Moto3 | Honda | +0.635 |
| 11 | 
Gabriel Rodrigo |
RBA Racing Team | KTM | +0.682 |
| 12 |
Adrián Martín |
MAPFRE Team MAHINDRA | Mahindra | +0.714 |
| 13 |
Andrea Locatelli |
Leopard Racing | KTM | +0.722 |
| 14 |
Niccolo Antonelli |
Ongetta-Rivacold | Honda | +0.735 |
| 15 | 
Jules Danilo |
Ongetta-Rivacold | Honda | +0.824 |
| 16 |
Joan Mir |
Leopard Racing | KTM | +0.893 |
| 17 |
Lorenzo Dalla Porta |
SKY Racing Team VR46 | KTM | +0.947 |
| 18 | 
Livio Loi |
RW Racing GP BV | Honda | +0.950 |
| 19 |
Fabio Quartararo |
Leopard Racing | KTM | +1.092 |
| 20 |
Stefano Manzi |
Mahindra Racing | Mahindra | +1.286 |
| 21 | 
Bo Bendsneyder |
Red Bull KTM Ajo | KTM | +1.363 |
| 22 |
Andrea Migno |
SKY Racing Team VR46 | KTM | +1.370 |
| 23 |
María Herrera |
Team Laglisse | Honda | +1.395 |
| 24 | 
Adam Norrodin |
Drive M7 SIC Racing Team | Honda | +1.583 |
| 25 |
Francesco Bagnaia |
ASPAR Mahindra Team Moto3 | Mahindra | +1.593 |
| 26 |
Albert Arenas |
Peugeot MC Saxo | Albert Arenas | +1.622 |
| 27 |
Khairul Idham Pawi |
Honda Team Asia | Honda | +1.807 |
| 28 |
Marcos Ramírez |
Platinum Bay Real Estate | Mahindra | +1.813 |
| 29 | 
John Mcphee |
SaxoPrint RTG | Peugeot | +1.894 |
| 30 |
Tatsuki Suzuki |
CIP | Mahindra | +1.916 |
| 31 |
Stefano Valtulini |
3570 Team Italia | Stefano Valtulini | +2.315 |
| 32 |
Lorenzo Petrarca |
3570 Team Italia | Stefano Valtulini | +2.342 |
| 33 |
Darryn Binder |
Platinum Bay Real Estate | Mahindra | +2.503 |
| 34 |
Fabio Spiranelli |
CIP | Mahindra | +3.289 |
| 35 | 
Alex Fabbri |
+3.735 |