The Repsol Honda rider won on this tight, twisty circuit in 2010 and 2011, but has yet to taste victory this season and needs to stay in touch with MotoGP World Championship leaders Casey Stoner and Jorge Lorenzo.
The Spaniard got his weekend off to the perfect start by topping the times, edging out team-mate Stoner late in the first session before again striking late as a mixture of rain and strong winds hampered the teams during the afternoon running.
The unhelpful track conditions later in the day meant the times from the morning session were the quickest during Friday's running.
Stoner, fresh from his victory in the Dutch TT last weekend, had looked set to lead the way but Pedrosa's final flying lap saw him record a time of one minute 22.357 seconds to edge the Australian by just. 0.087secs.
Lorenzo, who saw his championship lead go up in smoke thanks to his first corner fall in Assen, was never quite on the pace of the Hondas but the Yamaha man ended the day third quickest, less than three tenths of a second behind Pedrosa.
The Tech 3 Yamaha squad's early season form showed no signs of abating as Andrea Dovizioso sealed fourth place, with British team-mate Cal Crutchlow fifth despite still riding with the fractured ankle he suffered at Silverstone.
Hector Barbera was the top Ducati in sixth, beating the factory bikes of Nicky Hayden and Valentino Rossi, who could only manage seventh and 11th places respectively.
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Another poor performance that will not help to quell rumours that Rossi will return to Honda when Stoner retires at the end of the year, although Pedrosa and Moto 2 star Marc Marquez are tipped to land the two Repsol seats.
Alvaro Bautista, who will start from the back of the grid for his involvement in Lorenzo's Assen crash, was eighth, with home favourite Stefan Bradl and Ben Spies rounding out the top 10.
Speed Master Aprilia rider Mattia Pasini went to hospital for checks after suffering a bizarre fall in the morning session when a mechanic walked out in front of him in the pitlane, but the Italian was fit enough to ride towards the end of the afternoon's running.
Lorenzo, who needed the help of crutches to walk due to the ankle injury he sustained in Holland, declared himself satisfied with his day's work.
"I have more pain walking than on the bike which is good and adrenaline helps with it too," he said.
"I'm not 100% and I get more tired in the upper body compensating but I think we still did a good job this morning and this afternoon.
"The injury, the loss of points and the loss of the engine makes it more difficult for the championship but this just gives me more motivation to keep working and come back stronger to win."