Hasil Kualifikasi Moto3 Jepang 2018, Sabtu 20 Oktober 2018
| Pos. | Num. | Pembalap | Negara | Tim | Motor | Km/h | Waktu | Gap 1st/Prev. |
| 1 | 19 | Gabriel RODRIGO | ARG | RBA BOE Skull Rider | KTM | 216.1 | 1’56.894 | |
| 2 | 17 | John MCPHEE | GBR | CIP – Green Power | KTM | 216 | 1’56.969 | 0.075 / 0.075 |
| 3 | 12 | Marco BEZZECCHI | ITA | Redox PruestelGP | KTM | 218.8 | 1’57.014 | 0.120 / 0.045 |
| 4 | 88 | Jorge MARTIN | SPA | Del Conca Gresini Moto3 | Honda | 213.2 | 1’57.118 | 0.224 / 0.104 |
| 5 | 40 | Darryn BINDER | RSA | Red Bull KTM Ajo | KTM | 214.7 | 1’57.120 | 0.226 / 0.002 |
| 6 | 33 | Enea BASTIANINI | ITA | Leopard Racing | Honda | 217.7 | 1’57.194 | 0.300 / 0.074 |
| 7 | 10 | Dennis FOGGIA | ITA | SKY Racing Team VR46 | KTM | 215.5 | 1’57.202 | 0.308 / 0.008 |
| 8 | 22 | Kazuki MASAKI | JPN | RBA BOE Skull Rider | KTM | 219.3 | 1’57.260 | 0.366 / 0.058 |
| 9 | 75 | Albert ARENAS | SPA | Angel Nieto Team Moto3 | KTM | 216.9 | 1’57.410 | 0.516 / 0.150 |
| 10 | 48 | Lorenzo DALLA PORTA | ITA | Leopard Racing | Honda | 217.1 | 1’57.453 | 0.559 / 0.043 |
| 11 | 42 | Marcos RAMIREZ | SPA | Bester Capital Dubai | KTM | 216.4 | 1’57.476 | 0.582 / 0.023 |
| 12 | 14 | Tony ARBOLINO | ITA | Marinelli Snipers Team | Honda | 217.8 | 1’57.507 | 0.613 / 0.031 |
| 13 | 71 | Ayumu SASAKI | JPN | Petronas Sprinta Racing | Honda | 218 | 1’57.610 | 0.716 / 0.103 |
| 14 | 77 | Vicente PEREZ | SPA | Reale Avintia Academy 77 | KTM | 221.4 | 1’57.627 | 0.733 / 0.017 |
| 15 | 21 | Fabio DI GIANNANTONIO | ITA | Del Conca Gresini Moto3 | Honda | 216 | 1’57.636 | 0.742 / 0.009 |
| 16 | 84 | Jakub KORNFEIL | CZE | Redox PruestelGP | KTM | 213.6 | 1’57.692 | 0.798 / 0.056 |
| 17 | 23 | Niccolò ANTONELLI | ITA | SIC58 Squadra Corse | Honda | 215.8 | 1’57.755 | 0.861 / 0.063 |
| 18 | 16 | Andrea MIGNO | ITA | Angel Nieto Team Moto3 | KTM | 214.3 | 1’57.862 | 0.968 / 0.107 |
| 19 | 44 | Aron CANET | SPA | Estrella Galicia 0,0 | Honda | 215.2 | 1’57.910 | 1.016 / 0.048 |
| 20 | 72 | Alonso LOPEZ | SPA | Estrella Galicia 0,0 | Honda | 213.6 | 1’58.002 | 1.108 / 0.092 |
| 21 | 5 | Jaume MASIA | SPA | Bester Capital Dubai | KTM | 215.8 | 1’58.020 | 1.126 / 0.018 |
| 22 | 65 | Philipp OETTL | GER | Sudmetal Schedl GP Racing | KTM | 216.2 | 1’58.034 | 1.140 / 0.014 |
| 23 | 7 | Adam NORRODIN | MAL | Petronas Sprinta Racing | Honda | 215.5 | 1’58.107 | 1.213 / 0.073 |
| 24 | 31 | Celestino VIETTI | ITA | SKY Racing Team VR46 | KTM | 217.1 | 1’58.236 | 1.342 / 0.129 |
| 25 | 81 | Stefano NEPA | ITA | CIP – Green Power | KTM | 216.9 | 1’58.315 | 1.421 / 0.079 |
| 26 | 24 | Tatsuki SUZUKI | JPN | SIC58 Squadra Corse | Honda | 213.4 | 1’58.411 | 1.517 / 0.096 |
| 27 | 41 | Nakarin ATIRATPHUVAPAT | THA | Honda Team Asia | Honda | 215.8 | 1’58.659 | 1.765 / 0.248 |
| 28 | 27 | Kaito TOBA | JPN | Honda Team Asia | Honda | 216.7 | 1’58.659 | 1.765 |
| 29 | 13 | Shizuka OKAZAKI | JPN | Kohara Racing Team | Honda | 203.6 | 2’03.453 | 6.559 / 4.794 |
| 30 | 36 | Yuto FUKUSHIMA | JPN | Team Plus One | Honda | 201.1 | 2’03.584 | 6.690 / 0.131 |
