Kaepernick was the first NFL player to protest police brutality and racial injustice during the national anthem.
Trump also called the Nike campaign "a terrible" message in an interview with the Daily Caller, saying "maybe there's a reason for them doing it, but I think as far as sending a message, I think it's a bad message and a message that shouldn't be sent".
Nike gained 170,000 Instagram followers, and an Instagram post featuring Kaepernick was the second-most liked post in Nike's history, behind a post about the World Cup.
"Believe in something. Even if it means sacrificing everything", the ad read, with the words printed across a close up of Kaepernick's face.
Adding, "My dad to this day he doesn't really talk about the Vietnam War because that is something that these guys and women go to that us out here that are living an incredible life will never understand".
"But as for putting Colin Kaepernick's name alongside the Nike swoosh, voters say, 'Just do it'".
The company's stock rose as high as $83.90, surpassing its previous record, before closing at $83.47 on Thursday.
Nike, which has stood by other athletes involved in controversies such as golfer Tiger Woods, is one of the few brands that is highly rated by consumers across demographic categories, said Prophet Chief Growth Officer Scott Davis.
"Nike is getting absolutely killed with anger and boycotts", Trump tweeted. 'I wonder if they had any idea that it would be this way?
An Alabama pastor on Sunday used a pair of scissors during a sermon to destroy Nike items after learning the apparel company endorsed Colin Kaepernick. ESPN business insider Darren Rovell revealed just how the ads impacted Nike as a company.
'There was speculation that the Nike/Kaepernick campaign would lead to a drop in sales but the data does not support that theory, ' Edison Trends said through a spokesman. Gerzema said it helped Nike catch up, in the positive perception category, to Under Armour (57 percent) and Adidas (61 percent). Since Nike announced the campaign on Labor Day, shares are up about 4 percent.