Nike announced on Monday that Kaepernick would be one of the faces of the company's 30th anniversary of its "Just Do It" campaign, along with other athletes such as Serena Williams and LeBron James.
Kaepernick has made headlines since 2016 when he did not stand for the national anthem during a preseason game, initiating a wave of both similar protests as well as backlash. He is currently not signed to any NFL team after playing for the San Francisco 49ers for six seasons.
"I think it's a terrible message and a message that shouldn't be sent," Trump said in the interview. "There's no reason for it."
Trump described Nike as "a tenant of mine" that "pays a lot of rent." But the NikeTown store in New York City that the president was referencing is actually closed.
Despite his opposition, Trump also acknowledged that Nike's decision is a testament to the country's values.
"In another way, it is what this country is all about, that you have certain freedoms to do things that other people think you shouldn't do," he said. "But I personally am on a different side of it."
Shares of Nike closed down over 3 percent on Tuesday at $79.60 per share.