| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Marc Marquez | Repsol Honda | 289.6 | 01:33.556 | ||||
| 2 | Michele Pirro* | Ducati | 294.5 | 01:33.988 | 0.432 / 0.432 | |||
| 3 | Andrea Dovizioso | Ducati | 289.9 | 01:34.175 | 0.619 / 0.187 | |||
| 4 | Cal Crutchlow | LCR Honda | 291.1 | 01:34.196 | 0.640 / 0.021 | |||
| 5 | Danilo Petrucci | Octo Pramac Racing | 290.8 | 01:34.219 | 0.663 / 0.023 | |||
| 6 | Jorge Lorenzo | Ducati | 290.0 | 01:34.498 | 0.942 / 0.279 | |||
| 7 | Dani Pedrosa | Repsol Honda | 293.4 | 01:34.545 | 0.989 / 0.047 | |||
| 8 | Maverick Viñales | Movistar Yamaha | 291.1 | 01:34.592 | 1.036 / 0.047 | |||
| 9 | Johann Zarco | Tech 3 | 287.5 | 01:34.702 | 1.146 / 0.110 | |||
| 10 | Jonas Folger | Tech 3 | 289.0 | 01:34.786 | 1.230 / 0.084 | |||
| 11 | Hector Barbera | Reale Avintia Racing | 294.1 | 01:34.835 | 1.279 / 0.049 | |||
| 12 | Alvaro Bautista | Pull&Bear Aspar | 294.2 | 01:34.926 | 1.370 / 0.091 | |||
| 13 | Jack Miller | EG 0,0 Marc VDS | 287.4 | 01:34.953 | 1.397 / 0.027 | |||
| 14 | Aleix Espargaro | Aprilia Gresini | 283.6 | 01:35.160 | 1.604 / 0.207 | |||
| 15 | Tito Rabat | EG 0,0 Marc VDS | 289.8 | 01:35.243 | 1.687 / 0.083 | |||
| 16 | Andrea Iannone | Suzuki Ecstar | 287.0 | 01:35.306 | 1.750 / 0.063 | |||
| 17 | Alex Rins | Suzuki Ecstar | 287.4 | 01:35.415 | 1.859 / 0.109 | |||
| 18 | Scott Redding | Octo Pramac Racing | 287.2 | 01:35.536 | 1.980 / 0.121 | |||
| 19 | Pol Espargaro | Red Bull KTM | 290.0 | 01:35.625 | 2.069 / 0.089 | |||
| 20 | Loris Baz | Reale Avintia Racing | 284.7 | 01:35.655 | 2.099 / 0.030 | |||
| 21 | Bradley Smith | Red Bull KTM | 286.8 | 01:35.957 | 2.401 / 0.302 | |||
| 22 | Karel Abraham | Pull&Bear Aspar | 289.8 | 01:37.112 | 3.556 / 1.155 | |||
| 23 | Sam Lowes | Aprilia Gresini | 280.6 | 01:37.649 | 4.093 / 0.537 |
*Wild card entry
Note: Movistar Yamaha MotoGP rider Valentino Rossi did not take part in the San Marino Grand Prix after breaking his tibia and fibula in a training crash