His latest refusal to stand for the anthem -- he has done this in at least one other preseason game -- came before the 49ers' preseason loss to Green Bay at Levi's Stadium on Friday night.
"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 told NFL Media in an exclusive interview after the game. "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."
The 49ers issued a statement about Kaepernick's decision: "The national anthem is and always will be a special part of the pre-game ceremony. 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 and participate, or not, in our celebration of the national anthem."
Niners coach Chip Kelly told reporters Saturday that Kaepernick's decision not to stand during the national anthem is "his right as a citizen" and said "it's not my right to tell him not to do something."
The NFL also released a statement, obtained by NFL Media Insider Ian Rapoport: "Players are encouraged but not required to stand during the playing of the national anthem."
By taking a stand for civil rights, Kaepernick, 28, joins other athletes, like the NBA's Dwyane Wade, Chris Paul, LeBron James and Carmelo Anthony and several WNBA players in using their platform and status to raise awareness to issues affecting minorities in the U.S.
However, refusal to support the American flag as a means to take a stand has brought incredible backlash before and likely will in this instance. The NBA's Mahmoud Abdul-Rauf of the Denver Nuggets, formerly Chris Jackson before converting to Islam, refused to acknowledge the flag in protest, citing similar reasons as Kaepernick and saying that it conflicted with some of his Islamic beliefs.
Abdul-Rauf drew the ire of fans and was briefly suspended by the NBA before a compromise was worked out between the league and player, who eventually stood with his teammates and coaches at the playing of the national anthem.
Kaepernick said that he is aware of what he is doing and that he knows it will not sit well with a lot of people, including the 49ers. He said that he did not inform the club or anyone affiliated with the team of his intentions to protest the national anthem.
"This is not something that I am going to run by anybody," he said. "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 said that he has thought about going public with his feelings for a while but that "I felt that I needed to understand the situation better."
He said that he has discussed his feelings with his family and, after months of witnessing some of the civil unrest in the U.S., decided to be more active and involved in rights for black people. Kaepernick, who is biracial, was adopted and raised by white parents and siblings.
Kaepernick's Twitter feed is filled with civil rights messages.
The former Super Bowl starting quarterback's decision to go public comes while he is fighting for his football life with the 49ers, who drafted him in the second round in 2011. He lost his starting job last season after being one of the most promising players in the NFL during his run under former coach Jim Harbaugh.
Over the past few months, his relationship with management has turned sour. He requested a trade last spring, which never came. He also has spent most of the offseason rehabilitating from operations to his left (non-throwing) shoulder, his hand and knee. His recovery left him unable to fully compete with Blaine Gabbert for months and has him seemingly in a bind to regain his starting job.
He made his preseason debut against the Packers and played in the second quarter, completing two of six passes for 14 yards. He looked as rusty as you'd expect from someone who has not played since last November.
Following the game, and without any knowledge of Kaepernick's non-football behavior, coach Chip Kelly said that there has never been any discussion about cutting Kaepernick. Rapoport added Saturday that Kelly will make "football decisions" on Kaepernick, despite the quarterback's comments.