"I don't like what Nike did. I don't think it's appropriate," Trump told Fox News' "Fox & Friends" in an interview that aired Friday. "I honor the flag. I honor our national anthem."
When asked who was going to win the "cultural showdown," Trump said, during the Fox News interview before a crowd in Montana Thursday evening, "We are."
On Tuesday, Trump told conservative website The Daily Caller that Nike's Kaepernick ad sent a "terrible message."
Nike was not immediately available to respond to CNBC's request for comment on the president's remarks.
While a member of the 49ers in 2016, Kaepernick started kneeling during the national anthem to protest the treatment of African-Americans in the United States, which received mixed reactions.
Other athletes later joined in his protest, sparking a controversy that has been linked to declining television ratings for National Football League games.
The divisive issue came to a head after the conclusion of the 2017-2018 season.
In May, the NFL banned on-field kneeling during the anthem but allowed for players who don't want to stand to stay in the locker room until the anthem is over.
At the time, Trump also got involved, blasting players on Twitter who chose to kneel and the teams that supported the players' right to express themselves.
"Honestly, I don't know what the NFL is doing," Trump told Fox News. "From what I understand, it's in their contracts that you have to stand for the national anthem."
"I don't know why they're not enforcing it," he said, referring to the locker room option.
The 30th anniversary "Just Do It" ad, narrated by Kaepernick, was shown Thursday evening during the NFL season's kickoff, which featured the Atlanta Falcons taking on the Super Bowl champion Philadelphia Eagles.