Coach Chip Kelly told reporters Friday the quarterback is dealing with "arm fatigue."
Kaepernick will be limited in practice on Friday after taking Thursday off. Kelly said he's hopeful the quarterback can go in the preseason opener Sunday versus the Houston Texans.
"Just getting him back up to throwing every day. That's why we had planned on actually taking yesterday off," Kelly said. "We knew that going in, he didn't throw during the spring full, because of coming off of it (surgery) so it's just trying to get his arm back up to where we can just use him every day. If we've got to take a day off in between, it's not a real big deal."
Kaepernick underwent shoulder surgery among a trio of offseason operations. He sat out much of offseason work before getting cleared for training camp.
"I think he feels fine. He's dealt with it before. Just a little shoulder soreness," Kelly added.
Entering his sixth season, Kaepernick is in a heated battle with Blaine Gabbert to win the starting quarterback job.
Kelly said that Gabbert will start the preseason opener. Assuming Kaepernick plays, he'll follow.