The 23-year-old Visma–Lease a Bike rider finished ahead of France’s Paul Magnier and Australia’s Jensen Plowright to claim his fifth career stage win in Poland’s biggest annual cycling race.
With the victory, Kooij took the leader’s yellow jersey.
Poland’s top finisher, Stanisław Aniołkowski, placed sixth.
The second leg of the 82nd Tour de Pologne will see cyclists cover a 150 km route starting and ending in the mountain resort of Karpacz.
Nearly 170 riders from 22 international teams are taking part in the seven-stage 1,076-kilometre race, which runs until Sunday.
Top Polish cyclists Rafał Majka and Michał Kwiatkowski are among this year’s competitors.
Denmark’s Jonas Vingegaard won last year's Tour de Pologne.
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Source: IAR, PAP