Calificación Moto3 - Gran Premio de República Checa 2016
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Brad Binder |
Red Bull KTM Ajo | KTM | 2:07.785 |
| 2 | 
Andrea Migno |
SKY Racing Team VR46 | KTM | +0.158 |
| 3 |
Enea Bastianini |
Gresini Racing Moto3 | Honda | +0.257 |
| 4 | 
Adrián Martín |
MAPFRE Team MAHINDRA | Mahindra | +0.353 |
| 5 |
Fabio Di Giannantonio |
Gresini Racing Moto3 | Honda | +0.472 |
| 6 |
Nicolo Bulega |
SKY Racing Team VR46 | KTM | +0.548 |
| 7 |
Niccolo Antonelli |
Ongetta-Rivacold | Honda | +0.552 |
| 8 | 
Philipp Oettl |
Schedl GP Racing | KTM | +0.667 |
| 9 |
Arón Canet |
Estrella Galicia 0,0 | Honda | +0.710 |
| 10 | 
Jakub Kornfeil |
Drive M7 SIC Racing Team | Honda | +0.711 |
| 11 | 
John Mcphee |
SaxoPrint RTG | Peugeot | +0.774 |
| 12 |
Jorge Navarro |
Estrella Galicia 0,0 | Honda | +0.796 |
| 13 |
Karel Hanika |
Platinum Bay Real Estate | Mahindra | +0.817 |
| 14 |
Joan Mir |
Leopard Racing | KTM | +0.828 |
| 15 |
Juanfran Guevara |
RBA Racing Team | KTM | +0.979 |
| 16 | 
Fabio Quartararo |
Leopard Racing | KTM | +1.004 |
| 17 |
Francesco Bagnaia |
ASPAR Mahindra Team Moto3 | Mahindra | +1.023 |
| 18 | 
Hiroki Ono |
Honda Team Asia | Honda | +1.151 |
| 19 |
Andrea Locatelli |
Leopard Racing | KTM | +1.210 |
| 20 | 
Livio Loi |
RW Racing GP BV | Honda | +1.227 |
| 21 | 
Adam Norrodin |
Drive M7 SIC Racing Team | Honda | +1.279 |
| 22 | 
Gabriel Rodrigo |
RBA Racing Team | KTM | +1.336 |
| 23 |
Darryn Binder |
Platinum Bay Real Estate | Mahindra | +1.346 |
| 24 |
Jules Danilo |
Ongetta-Rivacold | Honda | +1.465 |
| 25 | 
Bo Bendsneyder |
Red Bull KTM Ajo | KTM | +1.473 |
| 26 |
Tatsuki Suzuki |
CIP | Mahindra | +1.502 |
| 27 |
Albert Arenas |
Peugeot MC Saxo | Albert Arenas | +1.766 |
| 28 |
María Herrera |
Team Laglisse | Honda | +1.866 |
| 29 |
Khairul Idham Pawi |
Honda Team Asia | Honda | +1.954 |
| 30 |
Marcos Ramírez |
Platinum Bay Real Estate | Mahindra | +2.156 |
| 31 |
Stefano Valtulini |
3570 Team Italia | Stefano Valtulini | +2.819 |
| 32 |
Lorenzo Petrarca |
3570 Team Italia | Stefano Valtulini | +3.405 |
| 33 |
Fabio Spiranelli |
CIP | Mahindra | +3.548 |