Jack Miller heeft in Sepang zijn achtste pole position van het seizoen gescoord. De Red Bull KTM coureur, die het volgend seizoen de overstap naar de MotoGP gaat maken, reed in de kwalificatie met 2'12.450 een nieuw absoluut ronderecord en was daarmee bijna een halve seconde sneller dan John McPhee. Jakub Kornfeil maakte de eerste startrij compleet.
| 1 | Jack MILLER | AUS | Red Bull KTM Ajo | KTM | 2'12.450 | |
| 2 | John MCPHEE | GBR | SaxoPrint-RTG | Honda | 2'12.909 | 0.459 / 0.459 |
| 3 | Jakub KORNFEIL | CZE | Calvo Team | KTM | 2'13.016 | 0.566 / 0.107 |
| 4 | Efren VAZQUEZ | SPA | SaxoPrint-RTG | Honda | 2'13.040 | 0.590 / 0.024 |
| 5 | Alex MARQUEZ | SPA | Estrella Galicia 0,0 | Honda | 2'13.315 | 0.865 / 0.275 |
| 6 | Romano FENATI | ITA | SKY Racing Team VR46 | KTM | 2'13.434 | 0.984 / 0.119 |
| 7 | Danny KENT | GBR | Red Bull Husqvarna Ajo | Husqvarna | 2'13.529 | 1.079 / 0.095 |
| 8 | Isaac VIÑALES | SPA | Calvo Team | KTM | 2'13.556 | 1.106 / 0.027 |
| 9 | Miguel OLIVEIRA | POR | Mahindra Racing | Mahindra | 2'13.679 | 1.229 / 0.123 |
| 10 | Enea BASTIANINI | ITA | Junior Team GO&FUN Moto3 | KTM | 2'13.709 | 1.259 / 0.030 |
| 11 | Alexis MASBOU | FRA | Ongetta-Rivacold | Honda | 2'13.822 | 1.372 / 0.113 |
| 12 | Karel HANIKA | CZE | Red Bull KTM Ajo | KTM | 2'13.884 | 1.434 / 0.062 |
| 13 | Niccolò ANTONELLI | ITA | Junior Team GO&FUN Moto3 | KTM | 2'13.990 | 1.540 / 0.106 |
| 14 | Niklas AJO | FIN | Avant Tecno Husqvarna Ajo | Husqvarna | 2'14.155 | 1.705 / 0.165 |
| 15 | Francesco BAGNAIA | ITA | SKY Racing Team VR46 | KTM | 2'14.290 | 1.840 / 0.135 |
| 16 | Hafiq AZMI | MAL | SIC-AJO | KTM | 2'14.413 | 1.963 / 0.123 |
| 17 | Alex RINS | SPA | Estrella Galicia 0,0 | Honda | 2'14.444 | 1.994 / 0.031 |
| 18 | Andrea MIGNO | ITA | Mahindra Racing | Mahindra | 2'14.796 | 2.346 / 0.352 |
| 19 | Juanfran GUEVARA | SPA | Mapfre Aspar Team Moto3 | Kalex KTM | 2'14.799 | 2.349 / 0.003 |
| 20 | Jorge NAVARRO | SPA | Marc VDS Racing Team | Kalex KTM | 2'15.277 | 2.827 / 0.478 |
| 21 | Ramdan ROSLI | MAL | Petronas AHM Malaysia | KTM | 2'15.455 | 3.005 / 0.178 |
| 22 | Zulfahmi KHAIRUDDIN | MAL | Ongetta-AirAsia | Honda | 2'15.498 | 3.048 / 0.043 |
| 23 | Matteo FERRARI | ITA | San Carlo Team Italia | Mahindra | 2'15.509 | 3.059 / 0.011 |
| 24 | Luca GRÜNWALD | GER | Kiefer Racing | Kalex KTM | 2'15.595 | 3.145 / 0.086 |
| 25 | Brad BINDER | RSA | Ambrogio Racing | Mahindra | 2'15.619 | 3.169 / 0.024 |
| 26 | Jules DANILO | FRA | Ambrogio Racing | Mahindra | 2'15.656 | 3.206 / 0.037 |
| 27 | Andrea LOCATELLI | ITA | San Carlo Team Italia | Mahindra | 2'15.750 | 3.300 / 0.094 |
| 28 | Alessandro TONUCCI | ITA | CIP | Mahindra | 2'15.828 | 3.378 / 0.078 |
| 29 | Remy GARDNER | AUS | Calvo Team | KTM | 2'15.875 | 3.425 / 0.047 |
| 30 | Philipp OETTL | GER | Interwetten Paddock Moto3 | Kalex KTM | 2'16.057 | 3.607 / 0.182 |
| 31 | Hafiza ROFA | MAL | SIC-AJO | KTM | 2'16.104 | 3.654 / 0.047 |
| 32 | Jasper IWEMA | NED | CIP | Mahindra | 2'16.253 | 3.803 / 0.149 |
| 33 | Scott DEROUE | NED | RW Racing GP | Kalex KTM | 2'16.326 | 3.876 / 0.073 |
| 34 | Gabriel RAMOS | VEN | Kiefer Racing | Kalex KTM | 2'16.929 | 4.479 / 0.603 |
