The 23-year-old Monegasque, born and bred in the Mediterranean principality, lapped the metal-fenced layout with a best time of one minute 11.684 seconds in the afternoon session.
Leclerc managed only four laps in the morning before being sidelined by a gearbox problem that left him bottom of those timesheets.
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Spanish team mate Carlos Sainz was second fastest, 0.112 slower, with Mercedes‘ seven-times world champion Lewis Hamilton third as Formula One returned to Monaco after two years’ absence due to COVID-19.
Red Bull’s Max Verstappen, 14 points adrift of Hamilton after four races, was fourth fastest.
It was the first time Ferrari had led a practice session since Sebastian Vettel, now at Aston Martin, was fastest in Hungary last July.
The afternoon session was stopped five minutes early after Mick Schumacher hit the barriers sideways at Massenet and parked up after going through the tunnel, with the Haas needing to be removed.
Mexican Sergio Perez was fastest for Red Bull in the opening session, the first time he had done so since joining the team this year.
The Mexican had a best time of 1:12.487 on the soft tyres, with Sainz again second quickest and 0.119 off the pace, with Verstappen third.
Hamilton, who has won three races to Verstappen’s one, was fifth on the morning timesheets and also on the medium tyres with team mate Valtteri Bottas sixth. AlphaTauri’s French driver Pierre Gasly was fourth fastest.
Two-times world champion Fernando Alonso hit the wall early on, smashing his front wing.
The race, a highlight of the calendar, was cancelled last year due to the pandemic but has returned with 40% capacity in the grandstands and 7,500 ticket holders a day.
Practice is traditionally on Thursday in Monaco rather than the usual Friday, which is a rest day for Formula One.