SANTA CLARA, Calif. — Colin Kaepernick will get one more chance to impress Coach Chip Kelly before the San Francisco 49ers announce their starting quarterback, even as the debate surrounding Kaepernick’s refusal to stand for the national anthem remains heated.

Kelly said Tuesday that Kaepernick will play in the team’s final exhibition game Thursday night in San Diego after missing the first two preseason games with a tired shoulder. This will be Kaepernick’s first game since he spoke publicly over his anthem protest, saying he won’t stand during the anthem because of what he described as oppression of minorities in the United States.

The 49ers declined to comment on whether there will be increased security in place for the game in San Diego, where Kaepernick has said he once again will sit during the national anthem.

Blaine Gabbert, who is also in the running for the starting job, won’t play because he has gotten 30 more plays in the preseason and Kelly does not need to evaluate him further.

Kelly said he will pick a starter for the regular-season opener against Los Angeles on Sept. 12 sometime after Thursday night’s game. He said Kaepernick remains one of his two best quarterbacks.

Despite that, Kelly said General Manager Trent Baalke will make the final call on whether Kaepernick remains on the team’s roster after the cut to 53 players on Saturday.

“It’s not up to me,” Kelly said.