ENGLEWOOD, Col. – Quarterback Colin Kaepernick did some light throwing on the side Wednesday while being held out of any passing drills in the 49ers' joint practice with the Denver Broncos.

Kaepernick might see an increase in his activity on Thursday, 49ers general manager Trent Baalke said.

“Right now, he’s being held back,” Baalke said. “You saw him out there. He threw a little bit today. He’ll throw possibly a little more tomorrow. And we’ll continue to bring him back as we see fit and as he sees fit.

“The medical staff is handling all of that stuff. I know he’s had consultations with the medical staff. Both the player and the medical staff feel good about where he’s at and what needs to be done.”

[MAIOCCO: 49ers practice 13: Things get chippy; Broncos land more blows]

Kaepernick has not participated in a practice since Aug. 10, when the 49ers held a practice at Kezar Stadium in San Francisco. Kaepernick struggled mightily with the velocity and accuracy of his passes.

The next day, coach Chip Kelly described Kaepernick's inactivity during practice as a planned rest day. But Kaepernick has not returned to practice, as he battles arm fatigue. It’s likely Kaepernick’s arm was not sufficiently strong enough to handle the workload -- from 86 to 102 pass attempts each day -- after rehabbing from offseason surgeries and not taking part in most of the team’s practices.


But why did it get to the point where Kaepernick had to be shut down for an entire week?

“Hindsight is always 20-20,” Baalke said. “This isn’t a case of, ‘Who made the mistake?’ A young man went out and his arm is tired. Rather than push it any further, just back it down and give him a little time to rest it. . We don’t have to be ready to play a game just yet. This is preseason football. You take care of each other during this time to get into the season as healthy and prepared as we can be.

“They’re working together very well, the medical staff and the player. You’re trying to point the finger here somewhere and there’s no finger to be pointed ... He knows his body better than anybody. He knows what he can push through and what he can’t push through. It’s very important for the medical staff and the player to work together and decide what the best course of action is moving forward. That’s what they’re doing.”

Although Baalke declined to speak specifically about Kaepernick’s condition, he disputed the notion that Kaepernick has a “dead arm.”

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“His arm is tired. To say it’s dead, I wouldn’t make that assumption,” Baalke said.

He added, “How much he throws tomorrow. How much the medical staff is willing to let him throw, all of that will be handled internally.”

Baalke also denied that he will be involved in the decision which quarterback will start other than his usual conversations with Kelly about the team's personnel. Blaine Gabbert continues to run with the first-team offense while Kaepernick rests. Gabbert and Kaepernick shared the first-team snaps during the first nine practices.

“The head coach is going to decide who the starting quarterback is for the San Francisco 49ers,” Baalke said.

Kaepernick’s situation is another turn in what has been an eventful year. In February, he requested permission to seek a trade. A possible deal to the Denver Broncos fell through because his agents could not work out an acceptable new contract and the 49ers would not pay a portion of his salary. Kaepernick’s $11.9 million base salary is fully guaranteed.

As the 49ers broke for the offseason, Kaepernick and Baalke had still not spoken, according to both men. On Wednesday, Baalke said the sides have gotten together.

“We sat down a couple of weeks ago,” Baalke said. “We had a good conversation. Colin is here to compete. All this stuff from the offseason, that’s behind us.”

Tune in tonight at 5 & 11 p.m. when I'll discuss this latest 49ers news out of Denver on SportsTalk Live, and also on SportsNet Central at 6 & 10:30 p.m. -- all on CSN Bay Area.