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Dow Jones first reported the hedge fund manager's move, saying his firm made around $100 million in profit from its investment in the athletic apparel and shoe company.
CNBC reported in January that Pershing Square started buying Nike in October when it was trading in the $52 to $53 per share range, according to a source.
Nike shares are up about 5 percent so far this year to roughly $66 per share. The company has a market value of nearly $107 billion.
It has been a difficult few years for Pershing Square's investors. The hedge fund's returns fell 4 percent in 2017, dropped 13.5 percent in 2016 and declined 20.5 percent in 2015, according to its website. The fund is down 6.2 percent so far this year as of March 20.
Nike shares are down 0.7 percent Thursday.
The company is slated to report its fiscal third-quarter financial results after the market close Thursday.
Pershing Square declined to comment.
— CNBC's Leslie Picker contributed to this story.