The former San Francisco 49ers quarterback has become one of the most talked-about figures in sport in the United States, since he became the first NFL player to kneel during the national anthem as a protest against injustice in the country.
In the ad, Kaepernick's face is shown with the words, "Believe in something".
The American football quarterback, 30, protested against racial injustice and police brutality by kneeling during the U.S. national anthem.
The irony of people discarding or defacing their (likely expensive) Nike merchandise to protest something they disagreed with was not lost on those who supported Kaepernick and his protests.
NFL owners approved a new policyin May which made it mandatory for all players on the field to stand during the pre-match ritual of the USA national anthem, albeit allowing them to stay in the locker room if they didn't wish to take part.
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"We commend Nike for its willingness to partake in a more edgy, risky advertising campaign while refreshing its 30-year old "Just Do It" campaign," Brian Nagel, an analyst at Oppenheimer wrote. Even so, the protests have persisted through the preseason and the National Football League has said it is in discussions with the players union on the policy.
Trump called Nike's campaign "a awful decision" in an interview with the Daily Caller published on Tuesday, but he also showed some respect for Kaepernick's right to speak out. But in the polarizing debate over NFL players taking a knee during the national anthem, Nike has made its bet. A choice few even turned to social media to post photos and videos of themselves burning and destroying their Nike gear.
The US leader has repeated those criticisms frequently over the past year, even suggesting at one stage that protesting players "shouldn't be in the country".