Within hours of the ad's big reveal showing an intense black and white shot of Kaepernick over which are superimposed the words, "Believe in something".
Analysts have predicted Trump is likely to step up his rhetoric against protesting players in an attempt to rally supporters ahead of November's mid-term elections.
With less than a week remaining before the kickoff of the National Football League season, Nike had quarterback-turned-lightning rod Colin Kaepernick reveal he was the face of the company's new "Just Do It" advertising campaign with a Monday afternoon Twitter post. "They pay a lot of rent", Mr Trump said during an interview with the Daily Caller on Tuesday, referring to Niketown New York. Vice President Mike Pence walked out of an Indianapolis Colts game after some players knelt.
Critics of Kaepernick, who have framed his protest as unpatriotic and disrespectful to the U.S. military, took to Twitter on Monday to hit out at the Nike deal.
Nike did not immediately respond to a request for comment.
Actor Zach Braff tweeted sarcastically: "Nike ran the numbers".
Since the release of a new Nike ad campaign featuring Colin Kaepernick Monday, many customers of the shoe giant have been destroying their apparel in a fiery protest of the partnership. It has been the key driving point for those that have chosen to send a message during the national anthem over the last couple of years since Kaepernick chose to do so.
President Donald Trump has slammed athletes who followed Kaepernick's lead.
They are still angry over the NFL's refusal to suspend players who abstained from standing for the national anthem last season.
John Brennan, a Central Intelligence Agency director from 2013-2017, tweeted his support, saying the athlete was a successful social justice campaigner.
"Soon, his one-man crusade spread throughout professional sports - leading to a massive backlash from patriotic fans", Starnes wrote, adding, "But Kaepernick stood his ground and became a revered character among America-hating leftists".