Defending MotoGP world champion Marquez failed to finished on the top step of the podium for the first time this season at the Czech Republic Grand Prix earlier this month, team-mate Dani Pedrosa preventing him from becoming the first man to win 11 straight premier-class races to start a campaign.
Marquez still heads the world championship by 77 points from Pedrosa and will be confident of extending that advantage following a strong performance in practice at Silverstone.
The Repsol Honda rider was fastest with a time of two minutes, 02.126secs, capping a fine day for the 21-year-old after he had headed the leaderboard in the first session.
LCR Honda's Stefan Bradl came in just over half a second slower, with Andrea Dovizioso rounding off the top three for Ducati.
There was good news for the British pairing of Bradley Smith and Scott Redding, who took fourth and sixth for Monster Yamaha Tech3 and GO&FUN Honda Gresini respectively.
Pramac Racing's Yonny Hernandez separated that duo as the Colombian ended the session in fifth.
But, while Marquez once again impressed, Pedrosa will have to improve if he is to stand a chance of cutting further into his team-mate's significant lead after he finished the second session a lowly ninth.
Meanwhile, it was a disappointing afternoon for Movistar Yamaha, whose riders Jorge Lorenzo and Valentino Rossi were only good enough for 11th and 13th.