Kaepernick, a social activist and former NFL quarterback, is blacklisted from the league for his participation in peaceful protests against police brutality.
Knight has been criticised on social media for agreeing to sing at the event while Kaepernick remains ousted from the game.
The singer has defended herself, saying she has fought inequality all her life. She says most of the people who criticise her want the right to sing the anthem.
“No matter who chooses to deflect with this narrative and continue to mix the two in the same message, it is not so and cannot be made so by anyone speaking it.”