After netting 12 goals in 31 games in the 1996–97 campaign, he transferred for €360,000 to Heerenveen the next year, and scored 13 goals in 31 matches in his only season with the club. He was then signed by PSV Eindhoven the next season for €6.3 million, a then-record transfer sum between two Dutch teams.
He scored 31 goals in 34 matches, the highest season total in the Eredivisie and second-highest in Europe overall, in addition to scoring all three of PSV's goals in a Champions League match against HJK Helsinki on 25 November 1998. Van Nistelrooy capped off the year by winning the Dutch Player of the Year award. The next season, he won his second Eredivisie scoring title with 29 goals. According to a 2001 interview with The Telegraph, Manchester United coach Alex Ferguson said that his son Darren, who was at tryouts for Eredivisie rival Heerenveen at the time, begged his father, "You've got to sign Van Nistelrooy right away, he's fantastic. We've been watching him." Ferguson sent team representatives to PSV's next league game and signed Van Nistelrooy the next day.