PSV was in urgent need of a replacement for Vennegoor of Hesselink, who had moved to Celtic in late August 2006. Just before the transfer deadline, PSV secured the services of the former Ajax player for one year. This transfer stirred controversy due to his past with the rival club. His debut took some time to materialize as he arrived at PSV unfit due to missing the preseason. It took a while for him to regain match fitness. He eventually made his debut against Feyenoord, but a week later, he suffered a right knee injury and had to go through rehabilitation again.
He returned in mid-December, at which point PSV had a comfortable lead over the competition. In the final weeks of the year, he made four appearances, scoring twice and providing three assists. After the winter break, Kluivert earned a starting spot, and the coach mentioned that PSV was stronger with Kluivert on the team. However, shortly after, he was mainly used as a pinch-hitter behind Arouna Koné by Ronald Koeman. When he suffered another injury, this time a back injury, confidence in the striker dwindled. Upon his return, he did manage to score against his former club, Ajax. With a difference in goal difference of only 1 goal, PSV snatched the title from Ajax at the last moment.
In addition to winning the league title, he reached the quarter-finals of the Champions League with PSV, where they were eliminated by Liverpool. Kluivert’s appearances in the Champions League were limited to three substitute appearances. His three goals and three assists in the league weren’t enough for an extended stay. In May 2007, it was announced that his contract would not be renewed.