The activist hedge fund will not pressure the shoe apparel company for changes, the source said. CNBC was not able to clarify the size of the hedge fund's position in Nike.
Pershing Square started buying Nike in October when it was trading in $52 to $53 per share range, according to a source. The stock closed at $67.71 Thursday.
Ackman's new stake was earlier reported by Reuters, which said it revealed at the firm's annual client dinner Thursday.
Nike shares are up 8 percent this month and have a market value of nearly $110 billion.
The passive investment fits with a sort of retreat from the public eye taking place right now by Ackman, the normally vocal activist. Reuters reported on Monday that Pershing Square is laying off 10 employees, representing nearly a fifth of its total staff. The hedge fund manager plans to spend more time investing and will stop marketing and public relations efforts, according to the report.
It has been a difficult three 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.
Nike shares are up 0.8 percent Friday morning.
— CNBC's Leslie Picker and Scott Wapner contributed to this story.