| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Marc Marquez | Repsol Honda | 309.8 | 01:54.596 | ||||
| 2 | Jorge Lorenzo | Movistar Yamaha | 308.9 | 01:54.849 | 0.253 / 0.253 | |||
| 3 | Andrea Iannone | Ducati | 312.4 | 01:55.227 | 0.631 / 0.378 | |||
| 4 | Aleix Espargaro | Suzuki Ecstar | 304.1 | 01:55.324 | 0.728 / 0.097 | |||
| 5 | Hector Barbera | Avintia Racing | 308.3 | 01:55.437 | 0.841 / 0.113 | |||
| 6 | Valentino Rossi | Movistar Yamaha | 308.0 | 01:55.509 | 0.913 / 0.072 | |||
| 7 | Andrea Dovizioso | Ducati | 309.8 | 01:55.748 | 1.152 / 0.239 | |||
| 8 | Maverick Viñales | Suzuki Ecstar | 307.7 | 01:55.787 | 1.191 / 0.039 | |||
| 9 | Dani Pedrosa+ | Repsol Honda | 310.7 | 01:55.841 | 1.245 / 0.054 | |||
| 10 | Cal Crutchlow | LCR Honda | 306.7 | 01:55.930 | 1.334 / 0.089 | |||
| 11 | Bradley Smith+ | Tech 3 | 305.4 | 01:56.115 | 1.519 / 0.185 | |||
| 12 | Pol Espargaro | Tech 3 | 308.7 | 01:56.522 | 1.926 / 0.407 |
+Riders advanced from Q1 to Q2
| 13 | Danilo Petrucci* | Octo Pramac Yakhnich | 307.1 | 01:56.148 | 0.355 / 0.291 | |||
| 14 | Scott Redding | Octo Pramac Yakhnich | 306.3 | 01:56.263 | 0.470 / 0.115 | |||
| 15 | Eugene Laverty | Pull & Bear Aspar | 308.9 | 01:56.535 | 0.742 / 0.272 | |||
| 16 | Stefan Bradl | Aprilia Gresini | 306.0 | 01:56.718 | 0.925 / 0.183 | |||
| 17 | Loris Baz | Avintia Racing | 303.7 | 01:56.797 | 1.004 / 0.079 | |||
| 18 | Yonny Hernandez | Pull & Bear Aspar | 305.2 | 01:56.805 | 1.012 / 0.008 | |||
| 19 | Alvaro Bautista | Aprilia Gresini | 304.7 | 01:57.062 | 1.269 / 0.257 | |||
| 20 | Tito Rabat | EG 0,0 Marc VDS | 307.0 | 01:57.606 | 1.813 / 0.544 |
*Three-place grid penalty, penalised for causing a collision with Aspar Team MotoGP rider Eugene Laverty on the last lap of the Austrian Grand Prix
Note: Team Estrella Galicia 0,0 Marc VDS rider Jack Miller did not take part in the Czech Republic Grand Prix due to injuries sustained in Austria
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