Los principales candidatos a la victoria en el Gran Premio de Aragón de MotoGP decidían no salir a la pista debido en el FP3 al mal estado de la misma. Esta circunstancia era aprovechada por Valentino Rossi para conseguir el mejor tiempo, por delante de Álvaro Bautista y de Nicky Hayden.
| POS | PILOTO | MOTO | TIEMPO/DIF |
| 1 | Valentino ROSSI | YAMAHA | 1'50.464 |
| 2 | Alvaro BAUTISTA | HONDA | 0.539 |
| 3 | Nicky HAYDEN | DUCATI | 1.081 |
| 4 | Aleix ESPARGARO | ART | 2.314 |
| 5 | Bradley SMITH | YAMAHA | 2.340 |
| 6 | Hiroshi AOYAMA | FTR | 2.742 |
| 7 | Andrea IANNONE | DUCATI | 3.041 |
| 8 | Yonny HERNANDEZ | DUCATI | 3.424 |
| 9 | Danilo PETRUCCI | IODA-SUTER | 3.482 |
| 10 | Luca SCASSA | ART | 4.029 |
| 11 | Claudio CORTI | FTR KAWASAKI | 4.637 |
| 12 | Bryan STARING | FTR HONDA | 4.968 |
| 13 | Randy DE PUNIET | ART | 5.563 |
| 14 | Michael LAVERTY | ART | 5.674 |
| 15 | Hector BARBERA | FTR | 6.826 |
| 16 | Colin EDWARDS | FTR KAWASAKI | 7.109 |
| POS | PILOTO | MOTO | TIEMPO/DIF |
| 1 | M.MARQUEZ | HONDA | 1'48.987 |
| 2 | S.BRADL | HONDA | 0.132 |
| 3 | D.PEDROSA | HONDA | 0.267 |
| 4 | J.LORENZO | YAMAHA | 0.418 |
| 5 | A.BAUTISTA | HONDA | 0.776 |
| 6 | C.CRUTCHLOW | YAMAHA | 0.853 |
| 7 | V.ROSSI | YAMAHA | 0.922 |
| 8 | A.DOVIZIOSO | DUCATI | 1.047 |
| 9 | A.ESPARGARO | ART | 1.068 |
| 10 | N.HAYDEN | DUCATI | 1.459 |
| 11 | A.IANNONE | DUCATI | 1.740 |
| 12 | H.BARBERA | FTR | 1.926 |
| 13 | B.SMITH | YAMAHA | 1.957 |
| 14 | Y.HERNANDEZ | DUCATI | 2.358 |
| 15 | C.CORTI | FTR KAWASAKI | 2.474 |
| 16 | R.DE PUNIET | ART | 2.712 |
| 17 | H.AOYAMA | FTR | 2.983 |
| 18 | C.EDWARDS | FTR KAWASAKI | 3.033 |
| 19 | D.PETRUCCI | IODA-SUTER | 3.134 |
| 20 | M.LAVERTY | ART | 4.233 |
| 21 | L.SCASSA | ART | 4.351 |
| 22 | B.STARING | FTR HONDA | 4.570 |
| 23 | L.PESEK | IODA-SUTER | 5.806 |
| 24 | D.CUDLIN | PBM | 6.356 |