Looking for a hat-trick win after claiming top podium spots at Catalunya and Mugello, Bagnaia broke the lap record clocked by fellow Italian rider Marco Bezzecchi in Assen last year.
With his best time of 1min 31.340sec, Bagnaia on a factory Ducati, led the way from veteran rider Maverick Vinales (Aprilia) and Marc Marquez (Gresini Racing Ducati) in windy first-day conditions on the legendary Dutch track.
"All the work done from the start of the season is starting to give us more feeling. I am very happy about it," Bagnaia told reporters afterwards.
Riding out for Friday's qualification, "Pecco" Bagnaia said he was "feeling that I was able to do what I wanted to do," with the factory Ducati.
But the wind made things tricky with riders battling to stabilise their machines.
Aleix Espargaro (Aprilia), suffered a heavy crash in the latter stages of Friday's qualifying, but was still fourth-fastest in his last-ever outing at Assen. The Spaniard is due to retire after a long MotoGP career at the end of this season.
Series leader Jorge Martin posted the fifth-fastest time -- two spots behind the season's current third placed and fellow Spanish rider Marquez.
The top 10 riders booked their place in Saturday's second qualifying session.
This group, which determines the first four rows of the grid, are joined by the two fastest riders from Q1.
Ahead of Saturday's sprint and Sunday's main event Bagnaia, second in the standings, is closing the gap with current leader Martin who is just 18 points ahead on 171.
Marquez is placed third, trailing 17 points behind Bagnaia, before this eighth round of the season.
Bagnaia, winner last weekend in Mugello, is seeking a third straight win at the "Cathedral".
Bagnaia won at Assen in 2022 and 2023, becoming the first to do so since his Italian compatriot and mentor Valentino Rossi claimed back-to-back victories here in 2004-2005.
In a year dominated by team changes, the Prima Pramac Racing Team on Friday announced they have signed a multi-year partnership with Yamaha and would be leaving the Ducati stable.
The decision comes in the wake of the announcement that the team was losing Martin, who will be joining Aprilia next year.
Prima Pramac are yet to announce their new riders for next year.
