| P | Rider | Team | Km/h | Lap time | Gap 1st/Prev. | |||
|---|---|---|---|---|---|---|---|---|
| 1 | Marc Marquez | Repsol Honda | 288.8 | 01:32.958 | ||||
| 2 | Maverick Viñales | Movistar Yamaha | 292.7 | 01:33.112 | 0.154 / 0.154 | |||
| 3 | Cal Crutchlow | LCR Honda | 291.7 | 01:33.240 | 0.282 / 0.128 | |||
| 4 | Andrea Dovizioso | Ducati | 290.2 | 01:33.334 | 0.376 / 0.094 | |||
| 5 | Jorge Lorenzo | Ducati | 292.2 | 01:33.414 | 0.456 / 0.080 | |||
| 6 | Johann Zarco | Tech 3 | 289.3 | 01:33.584 | 0.626 / 0.170 | |||
| 7 | Aleix Espargaro | Aprilia Gresini | 289.4 | 01:33.626 | 0.668 / 0.042 | |||
| 8 | Dani Pedrosa | Repsol Honda | 293.0 | 01:33.673 | 0.715 / 0.047 | |||
| 9 | Danilo Petrucci | Octo Pramac Racing | 291.3 | 01:33.802 | 0.844 / 0.129 | |||
| 10 | Michele Pirro* | Ducati | 293.0 | 01:33.836 | 0.878 / 0.034 | |||
| 11 | Jack Miller | EG 0,0 Marc VDS | 289.8 | 01:34.010 | 1.052 / 0.174 | |||
| 12 | Alvaro Bautista | Pull&Bear Aspar | 293.2 | 01:34.112 | 1.154 / 0.102 | |||
| 13 | Loris Baz | Reale Avintia Racing | 288.0 | 01:34.144 | 1.186 / 0.032 | |||
| 14 | Tito Rabat | EG 0,0 Marc VDS | 289.9 | 01:34.155 | 1.197 / 0.011 | |||
| 15 | Scott Redding | Octo Pramac Racing | 289.6 | 01:34.203 | 1.245 / 0.048 | |||
| 16 | Andrea Iannone | Suzuki Ecstar | 287.0 | 01:34.263 | 1.305 / 0.060 | |||
| 17 | Pol Espargaro | Red Bull KTM | 291.6 | 01:34.307 | 1.349 / 0.044 | |||
| 18 | Alex Rins | Suzuki Ecstar | 289.5 | 01:34.371 | 1.413 / 0.064 | |||
| 19 | Karel Abraham | Pull&Bear Aspar | 291.5 | 01:34.420 | 1.462 / 0.049 | |||
| 20 | Jonas Folger | Tech 3 | 288.1 | 01:34.532 | 1.574 / 0.112 | |||
| 21 | Hector Barbera | Reale Avintia Racing | 295.3 | 01:34.820 | 1.862 / 0.288 | |||
| 22 | Bradley Smith | Red Bull KTM | 290.7 | 01:35.021 | 2.063 / 0.201 | |||
| 23 | Sam Lowes | Aprilia Gresini | 281.7 | 01:35.132 | 2.174 / 0.111 |
*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