Leclerc was fastest after the first of three hours of practice ahead of Sunday’s Emilia Romagna Grand Prix.
He headed George Russell, Carlos Sainz, Sergio Perez and the frustrated Verstappen only fifth best.
The Dutchman struggled to string a lap together, losing time on his first qualifying simulation effort before mistakes on the two attempts that followed left him bashing the wheel of his RB20.
It was a busy start to the session with the entire field heading out soon after the pit lane opened.
That included Oliver Bearman, who’d taken the wheel of Kevin Magnussen’s Haas for the session.
Nine of the 10 teams have upgrades this weekend, the first day of European running in 2024.
All three compound tyres were in use, though only Red Bull Racing bolted on the softs initially.
Not everyone recorded a lap, McLaren cycling Lando Norris and Oscar Piastri back through the pits in the opening minutes before Piastri logged a 1:18.986s to go fastest.
Norris had an aero rake fitted to his car, McLaren having introduced a smaller upgrade package this weekend versus what it had in Miami.
The exit of Acque Minerali was proving tricky with a number of drivers running onto the reprofiled exit kerb.
A problem for Alex Albon saw the Williams driver roll to a halt exiting Acque Minerali after 19 minutes of running.
The Williams struck issues going into the complex and rolled to a halt – the car having shut down on the Thai-licenced driver – before he climbed out of the machine.
Running resumed six minutes later, Fernando Alonso and Lando Norris the first two cars back on track.
Times continued to tumble and Leclerc rose to the top of the timesheets on a 1:17.120s with Yuki Tsunoda slotting in second before the RB was bumped down the order as others improved.
Daniel Ricciardo in the sister car had a moment at Rivazza when he pinched a brake and slid into the gravel. He was able to release the brake and rejoin the track without further drama.
A moment for Hamilton saw the Mercedes driver come unstuck exiting the Acque Minerali after he tagged the apex kerb at the second part of the right-hander.
That pitched him into a spin from which he quickly recovered, another of the growing list of drivers to have moments on the unforgiving Imola circuit.
On his qualifying simulation with 12 minutes to run, Verstappen proved rapid through the first third of the lap but lost time during the middle sector.
It left him only fourth at the end of the lap, fifth once Sergio Perez flashed across the line moments later.
A second attempt soon after resulted in snap oversteer as Verstappen turned into the Variante Alta, forcing him to abandon the lap.
In the final minute, there was a second off for Verstappen as he ran long at Acque Minerali, doing well not to bury the Red Bull Racing in the gravel.
It left the championship leader bashing the wheel in frustration as his session ended with him fifth fastest.
Heading affairs was Leclerc from Russell, Sainz, Perez, Verstappen, Tsunoda, Hamilton, Norris, Piastri, and Alonso in the top 10.
Ricciardo slipped back to 13th, his best 1.152s away from the absolute pace and seven places back from his RB team-mate.
With teams working through their own upgrade assessment programme, and an array of tyre compounds in use, it was a difficult session to take much from.
However, the frustration at Red Bull Racing for Verstappen was palpable as he struggled to get a lap together, while Ferrari and Mercedes both appeared comfortable by comparison.
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