The Repsol Honda rider beat fellow Spaniard Jorge Lorenzo into second place in both sessions with the Yamaha rider crashing halfway through free practice two.
Pedrosa is currently 17 points behind Lorenzo in the driver's championship and will be looking to close the gap this weekend.
The 26-year-old's team-mate Casey Stoner will miss the Grand Prix to have surgery on an ankle injury and has already said he believes he is out of the championship picture.
Monster Yamaha Tech 3 riders Andrea Dovizioso and Cal Crutchlow occupied third and fourth place in second practice with the LCR Honda of Stefan Bradl in fifth.
Seven-time world champion Valentino Rossi had one of his best sessions of the season, finishing less than half a second slower than Pedrosa's fastest time, giving him sixth place.