Kaepernick sat on the team's bench Friday night during the anthem before the Niners played host to the Green Bay Packers in an exhibition game. He later explained his reasoning in an interview with NFL Media.
"I am not going to stand up to show pride in a flag for a country that oppresses black people and people of color," Kaepernick said. "To me, this is bigger than football and it would be selfish on my part to look the other way. There are bodies in the street and people getting paid leave and getting away with murder."
NFL spokesman Brian McCarthy said Saturday that "players are encouraged but not required to stand during the playing of the national anthem."
The 49ers issued a statement after Pro Football Talk initially reported on Kaepernick's stand, saying that Americans have the right to protest or support the anthem.
"The national anthem is and always will be a special part of the pregame ceremony," the team said. "It is an opportunity to honor our country and reflect on the great liberties we are afforded as its citizens. In respecting such American principles as freedom of religion and freedom of expression, we recognize the right of an individual to choose to participate, or not, in our celebration of the national anthem."
Coach Chip Kelly said Saturday that he had not talked with Kaepernick about his actions or comments but said that Kaepernick also did not stand for the national anthem before last week's game in Denver when he was injured and did not play.
"We recognize his right to do that," Kelly said. "It's not my right to tell him not to do something. That's his right as a citizen."
Kaepernick, who is biracial, was adopted and raised by white parents. He has been outspoken on his Twitter account on civil rights issues and in support of the Black Lives Matter movement.
"Players are encouraged but not required to stand during playing of national anthem." - NFL statement on Kaepernick pic.twitter.com/7DVhqzKCEQ— SportsCenter (@SportsCenter) August 27, 2016
Kaepernick is not the first U.S.-based athlete to use the anthem for protest. In 1996, NBA player Mahmoud Abdul-Rauf refused to stand for the anthem, saying the United States had a history of tyranny and doing so would conflict with his Islamist beliefs. The NBA initially suspended Abdul-Rauf for his stance before it was lifted when he said he would stand and pray silently during the song.
Kaepernick said he is not worried about any potential fallout from his protest.
"This is not something that I am going to run by anybody," he told NFL Media. "I am not looking for approval. I have to stand up for people that are oppressed. ... If they take football away, my endorsements from me, I know that I stood up for what is right."
Kaepernick's agent did not immediately return a request for comment.
Kaepernick is in competition to win back the starting quarterback job in San Francisco that he lost to Blaine Gabbert last season. He made his first appearance of the preseason on Friday night after missing two games with a tired shoulder. He finished 2 for 6 for 14 yards and added 18 yards on four runs.
Kelly said Kaepernick is still in the running to win the starting job and his protest won't impact the decision.
For more on the San Francisco 49ers, click here.
If you follow Kaepernick on IG, this isn't new news! He's had a not so gentle rage brewing for a very long time. https://t.co/dCtil4SkAL— Cari Champion (@CariChampion) August 27, 2016
Texts coming in from coaches, players, front office execs from around league on Kap. So far every player backs him. No coach/exec does.— mike freeman (@mikefreemanNFL) August 27, 2016
@swhitfield75 what does him making money have anything to do with it. He standing for what he believes is right. Can't put a price on it— Chris McCain (@DolphinEret) August 27, 2016
This guy is a joke. Get lost. You don't like it in a country that has given you opportunity to succeed? Then get out https://t.co/Dwssw2I1zA— AUBREY HUFF (@aubrey_huff) August 27, 2016
Activists changed USA for better but have to associate Nat Anthem w/ military that die for ur right to protest. Stand up. Find another way— Tyler Polumbus (@Tyler_Polumbus) August 27, 2016
The easy thing to do is to make fun of Kap and his play. How about trying to understand where he's coming from....but that would be too hard— Adrian Clayborn (@AJaClay) August 27, 2016
Kaep is using his platform & brand to make a compelling & polarizing point, which is his right, even if it's met with ire!#idontagree— Tiki Barber (@TikiBarber) August 27, 2016
I'm not saying Kaep is Ali at all but ppl vilified Ali for his stance as well & it wasn't until he couldn't speak that ppl celebrated him— Damien Woody (@damienwoody) August 27, 2016
Absolutely he is. It's a platform to use. They don't play the Natl Anthem during practice https://t.co/J41j40aV6p— Carp (@robcarpenter81) August 27, 2016
I will be STANDING during the National Anthem tonight. Thank you to ALL (Gender,Race,Religion)that put your lives on the line for that flag— Justin Pugh (@JustinPugh) August 27, 2016