Stoner, who triumphed in the wet at the Northamptonshire circuit a year ago en route to his second title, goes into the event with ground to make up in this season's championship.
The Australian has fallen 20 points adrift of Jorge Lorenzo in the wake of back-to-back wins for the Spaniard at Le Mans and on home soil in Barcelona a fortnight ago.
Stoner, however, on Friday looked impressive as wind, rain and the odd burst of sunshine hit Silverstone, with his best lap late in the second session with a time of two minutes 04.791secs on his Repsol Honda.
Lorenzo, who this week signed a new two-year deal to remain with the factory Yamaha outfit after spurning advances from Honda to replace Stoner when he retires at the end of this season, was down in seventh, 0.697secs adrift.
For once Lorenzo had to settle for second best to team-mate Ben Spies, who recovered from a crash in the wet in the morning run to finish second to Stoner, just 0.034secs down.
In between the duo were Honda's Alvaro Bautista, who like Spies also crashed in the morning, with Nicky Hayden the lead Ducati in fourth, just over half a second down on Stoner.
Germany's Stefan Bradl was fifth on his Honda, followed by the Yamaha of Andrea Dovizioso, fourth in the championship, 55 points behind Lorenzo.
Team-mate Cal Crutchlow, who with 56 points from five races has made the best start to a season at this level by a British rider since Ron Haslam in 1987, was down in eighth, 0.783secs off the pace.
Stoner's team-mate Dani Pedrosa, 30 points behind Lorenzo, was ninth quickest, with fellow Spaniard Hector Barbera on a Ducati completing the top 10.
Seven-times champion Valentino Rossi, quickest in the morning but 15 seconds slower than Stoner in the afternoon to highlight how conditions improved, eventually wound up 11th, 2.3secs down.
Watch: Stoner fastest at changeable Silverstone... More Videos
Czech rider Karel Abraham, meanwhile, has been ruled out of the weekend following final medical checks before practice.
The Ducati rider is sidelined with a double fracture of the little finger on his left hand sustained in a recent test crash.
Abraham said: "Doctors highly recommended I not race otherwise the broken bones could dislocate and mean that surgery will be necessary.
"This could endanger my start for the races that follow, so we can't risk it.
"It's really bad for us to lose a race, but it's certainly better than to lose four races in July. I really hope I will be back on track in two weeks (for the Dutch GP at Assen)."