The so-far unidentified woman was pictured kneeling before the team’s game against Oakland Raiders on Thursday.
The 49ers used to be the team of Colin Kaepernick who knelt during the anthem as a protest in 2016 to highlight police brutality against African-Americans.
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He was joined by his teammate Eric Reid, along with others in the league.
If the cheerleader did kneel in protest it would be the first time an NFL cheerleader has demonstrated this way.
The NFL protests began in 2016 when Kaepernick, who was then the 49ers’ quarterback, refused to stand for the anthem.
Other teams have protested with some linking arms in solidarity.
The action has been criticised by some fans and Donald Trump who said it was disrespectful and called them “sons of bitches”.
His remarks prompted a wave of further protests across the 2017 NFL season, putting several conservative Trump-supporting team owners in an awkward position.
In May, NFL chiefs ordered players to stand during the national anthem. They said players would also be allowed to remain in the locker room.
Kaepernick has been without a team since March of last year, and has filed a grievance claiming the league’s owners have been colluding to keep him out of work.
The NFL (National Football League) consists of 32 teams and is the highest professional level of American football in the world.
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