Adam Schefter explains why Colin Kaepernick's agents have requested a trade from the 49ers and how that affects San Francisco's plans at quarterback. (0:58)

SANTA CLARA, Calif. -- While new San Francisco 49ers coach Chip Kelly gave the impression Thursday that Colin Kaepernick wants to return to the team, sources told ESPN's Adam Caplan that Kaepernick's agents have requested permission from the team to seek a trade.

NFL Network first reported the trade request.

That would fly in the face of what Kelly, who chose to speak to beat writers in a private setting rather than at the open podium session, said earlier Thursday at the NFL combine.

"He wants to be here," Kelly told reporters. "He's never expressed to me that he didn't want to be here. He expressed to me that he's excited about getting healthy and getting going. And we're excited about him getting healthy and getting going."

Colin Kaepernick was benched last season after the 49ers' 2-6 start. His $11.9 million base salary for the 2016 season becomes guaranteed on April 1. AP Photo/Ben Margot

Kaepernick's future with the team appeared to be in limbo anyway. He is recovering from surgeries to his left shoulder, right thumb and left knee, and on April 1 his $11.9 million base salary for 2016 becomes guaranteed. There also is a seemingly growing distrust between player and organization after he was benched midway through the season and after a 2-6 start.

Kaepernick chose to have private doctors perform his procedures, rather than team doctors.

Still, Kelly told a different story earlier Thursday.

"He's seemed excited every time I've talked to him," Kelly said. "I've also learned to not believe everything that's on the Internet.

"There's a reason he was on IR. I mean, there was something wrong with him."

Kelly, like Niners general manager Trent Baalke a day earlier, also gave the impression he expected Kaepernick at the team facility for the beginning of the offseason training program on April 4, three days after Kaepernick's salary becomes guaranteed in case of injury.

"Kap's really good," Kelly said. "I mean, he had the ball on the 5-yard line [about] ... to win a Super Bowl. You can just look at the tape to see how talented he is. You know, our job is acquiring talent, not getting rid of talent."

Kelly drew some criticism during his stint with the Philadelphia Eagles after the manner in which he got rid of players such as DeSean Jackson, LeSean McCoy and Evan Mathis.

His praise of Kaepernick on Thursday contrasted with the lukewarm endorsement he gave at his introductory news conference, when Kelly also praised the job done by Blaine Gabbert.

"You've got to see them in general," Kelly said Thursday. "I think one of the misconceptions is how somebody can evaluate a tape and say, 'This guy made the wrong decision.' You don't know what the play call was."

And now Kelly might not know whether Kaepernick wants to play for him or wants to be traded away from the organization that drafted him in 2011.