Leclerc's team mate Sebastian Vettel was sidelined for most of the session after Ferrari detected something wrong with his car's intercooler system and made a decision to strip it down to be ready for the second session.
Hamilton, who on Sunday seeks a record-increasing seventh Silverstone victory, finished ahead of his Mercedes team-mate Valtteri Bottas by more than three-tenths of a second after the Finn had been fastest in final practice and then again in both Q2 and Q3 when he also set lap records.
Hamilton had said he felt compelled to speak out about a lack of leadership and unity and what he felt was an unnecessary "battle" to ensure the sport's anti-racism stance was pushed to the front of people's minds.
Mercedes' six-times world champion Lewis Hamilton, who will be chasing a record seventh home win, was second fastest, 0.474 off the pace but using slower medium tyres than the Dutchman's softs.
"That was less than 24 hours ago, so it feels a bit surreal for me right now, but I like a good challenge and this is certainly one", said the 32-year-old.
"Ultimately it's obviously a relatively big gap between us and third place", Hamilton told Jenson Button after the end of qualifying.
"I was one of the first ones to support and to push that we take the knee and I'm still hopeful that one day we will get 20 drivers to take the knee on the grid and that it will happen at one point".
"I made some changes before qualifying and it was worse".
"It was a real struggle out there", he told 2009 world champion and compatriot Jenson Button in an interview after stepping out of the black auto.
"This track is hard with the wind and it is like juggling balls while spinning plates at high speed".
"I was already down through the first section every lap and - I don't know how - but with some deep breaths managed to compose myself. It never gets old".