| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Marc Marquez | Repsol Honda | 277.1 | 01:48.170 | ||||
| 2 | Danilo Petrucci | Octo Pramac Racing | 276.9 | 01:49.164 | 0.994 / 0.994 | |||
| 3 | Loris Baz | Reale Avintia Racing | 271.4 | 01:49.246 | 1.076 / 0.082 | |||
| 4 | Jorge Lorenzo | Ducati | 275.7 | 01:49.280 | 1.110 / 0.034 | |||
| 5 | Cal Crutchlow | LCR Honda | 279.3 | 01:49.444 | 1.274 / 0.164 | |||
| 6 | Andrea Iannone | Suzuki Ecstar | 273.9 | 01:49.481 | 1.311 / 0.037 | |||
| 7 | Maverick Viñales | Movistar Yamaha | 277.7 | 01:49.509 | 1.339 / 0.028 | |||
| 8 | Andrea Dovizioso | Ducati | 277.1 | 01:49.703 | 1.533 / 0.194 | |||
| 9 | Sam Lowes | Aprilia Gresini | 272.5 | 01:49.961 | 1.791 / 0.258 | |||
| 10 | Scott Redding | Octo Pramac Racing | 272.0 | 01:50.162 | 1.992 / 0.201 | |||
| 11 | Alex Rins | Suzuki Ecstar | 274.8 | 01:50.245 | 2.075 / 0.083 | |||
| 12 | Jack Miller | EG 0,0 Marc VDS | 270.6 | 01:50.470 | 2.300 / 0.225 | |||
| 13 | Michele Pirro* | Ducati | 267.8 | 01:50.496 | 2.326 / 0.026 | |||
| 14 | Bradley Smith | Red Bull KTM | 270.4 | 01:50.827 | 2.657 / 0.331 | |||
| 15 | Aleix Espargaro | Aprilia Gresini | 268.9 | 01:51.021 | 2.851 / 0.194 | |||
| 16 | Pol Espargaro | Red Bull KTM | 275.6 | 01:51.079 | 2.909 / 0.058 | |||
| 17 | Jonas Folger | Tech 3 | 269.5 | 01:51.189 | 3.019 / 0.110 | |||
| 18 | Hector Barbera | Reale Avintia Racing | 276.0 | 01:51.276 | 3.106 / 0.087 | |||
| 19 | Tito Rabat | EG 0,0 Marc VDS | 271.5 | 01:51.900 | 3.730 / 0.624 | |||
| 20 | Johann Zarco | Tech 3 | 271.6 | 01:51.967 | 3.797 / 0.067 | |||
| 21 | Alvaro Bautista | Pull&Bear Aspar | 259.3 | 01:52.889 | 4.719 / 0.922 | |||
| 22 | Karel Abraham | Pull&Bear Aspar | 265.8 | 01:53.599 | 5.429 / 0.710 | |||
| 23 | Dani Pedrosa | Repsol Honda | 256.9 | 01:53.842 | 5.672 / 0.243 |
*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