Kaepernick was joined by teammate Eric Reid, who also dropped to one knee while Petty Officer 1st Class Steven Powell from the U.S. Navy sang "The Star-Spangled Banner." Also, simultaneously, 240 sailors, marines and soldiers unfurled an oversized flag at the Chargers' Qualcomm Stadium.
The pair were met with scattered boos during the anthem, but Kaepernick was met with significantly more boos in his snap of the game.
Kaepernick has said his protest will continue indefinitely.
"When there's significant change and I feel like the flag represents what it's supposed to represent in this country, I'll stand," he told reporters Sunday.
Tonight's game is particularly noteworthy because it is Military Night at Qualcomm Stadium, billed as a tribute to "hundreds of thousands of current and retired military personnel who live and work in San Diego," according to the San Diego Chargers' website.
Today, Kaepernick responded to critics who slammed him for wearing socks during a Aug. 10 practice with imagery of illustrated pigs wearing police hats. The term "pig" is a derogatory term for police officers.