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"Believe in something. Even if it means sacrificing everything," reads an ad Kaepernick shared on social media Monday.
Nike has kept Kaepernick on its endorsement roster over the years after signing him in 2011. He has not appeared in any of the brand's ads for the previous two years.
"We believe Colin is one of the most inspirational athletes of this generation, who has leveraged the power of sport to help move the world forward," Gino Fisanotti, Nike's vice president of brand for North America, told ESPN.
A source with knowledge of Nike's contract with Kaepernick told the Associated Press that the company will feature Kaepernick on several platforms, including billboards, television commercials and online ads. Nike also will create an apparel line for Kaepernick and contribute to his Know Your Rights charity.
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Other athletes in the "Just Do It" campaign include Odell Beckham Jr., Shaquem Griffin, Lacey Baker, Serena Williams and LeBron James.
Kaepernick is suing the NFL for allegedly colluding to keep him out of the league. An arbitrator sent Kaepernick's grievance with the NFL to trial, denying the league's request to throw out his claims that owners conspired to keep him out of the league because of his protests of social injustice.
Kaepernick began a wave of protests by NFL players two seasons ago, kneeling during the national anthem to protest police brutality and racial inequality. The protests have grown into one of the most polarizing issues in sports, with President Donald Trump loudly urging the league to suspend or fire players who demonstrate during the anthem.
ESPN contributed to this report.