Adam Schefter, Mark Dominik and Louis Riddick react to Colin Kaepernick opting out of his contract with the 49ers and examine what is next for Kaepernick and San Francisco. (1:50)

SANTA CLARA, Calif. -- For the first time in his NFL career, quarterback Colin Kaepernick will be a free agent.

Kaepernick is planning to opt out of the final season of his contract with the San Francisco 49ers on Thursday, a source told ESPN's Adam Schefter.

Colin Kaepernick' protests last season during the national anthem has led to similar league-wide actions by players this year. Thearon W. Henderson/Getty Images

The league was notified in a letter sent to all teams by Kaepernick's representation, Select Sports Group. Thursday is the first day Kaepernick can opt out, and he has until the new league year begins March 9 to do it.

Kaepernick's contract was originally supposed to keep him with the Niners through 2020, but the team worked with the 29-year-old to revamp it before he reclaimed the starting job in October.

As part of the deal's reconfiguration, Kaepernick traded $14.5 million in injury guarantees during the 2017 season for the opportunity to opt out of the deal early. His decision saves the Niners his $14.5 million base salary in 2017 though he will still count nearly $2.5 million in dead money for the remainder of his signing bonus proration.

From the moment Kaepernick and the Niners struck that agreement, the expectation was that Kaepernick would explore his options. Even if he elects to stay, the 49ers still would have the ability to release him with minimal salary cap repercussions.

Even after the restructure, Kaepernick insisted he wasn't thinking about anything beyond the season. At the end of the year, he expressed gratitude toward 49ers CEO Jed York and executive vice president Paraag Marathe.

"Once again, I have a great appreciation for this organization," Kaepernick said. "Jed and Paraag, I have a good relationship with them, so a lot of things to think about moving forward and we'll see where this goes."

That was the last time Kaepernick spoke with Bay Area media, and much changed in the days and weeks that followed. The 49ers fired general manager Trent Baalke and coach Chip Kelly and eventually hired John Lynch and Kyle Shanahan as their replacements.

Kaepernick reached out to Lynch, whom he had a previous relationship with from Lynch's time as a broadcaster. Shanahan and Lynch agreed to meet with Kaepernick, and Lynch told 95.7 The Game radio in late February he would give Kaepernick a fair shake in his evaluation.

"The one thing we will do very well with Kap is we'll communicate," Lynch said. "I think that's very important for both sides. Like everything else, that process is well in the works. We'll continue to do that and we'll be very up front with him."

Kaepernick started 11 games for the 49ers in 2016, posting his best statistical season since 2013 despite the team's 1-10 record in his starts. His 90.7 passer rating was his best in three years and ranked 17th in the NFL. His 4-1 touchdown-interception ratio was tied for sixth, his 468 rushing yards were second among quarterbacks and his 6.78 yards per carry were first. On the flip side, Kaepernick's 59.2 percent completion rate was 26th.

Of course, nothing Kaepernick did on the field registered in the way his protest of racial inequality did. As a means of protest, he began sitting during the national anthem in the preseason before taking a knee for the final preseason contest and 16 regular-season games. Kaepernick also vowed to donate $1 million plus proceeds from his jersey sales to various charities, a project he dubbed "The Million Dollar Pledge." He has followed through with monthly donations of $100,000 spread over 10 months to organizations all over the country.

At the end of the season, teammates recognized Kaepernick with the highest in-house honor a 49er can receive when they voted him the winner of the Len Eshmont Award. According to the team, the award goes to the 49er who "best exemplifies the inspirational and courageous play of Len Eshmont, an original member of the 1946 49ers team."

Lynch and Shanahan met with Kaepernick to discuss his future on Feb. 22, a conversation Lynch described as "positive." Earlier in the offseason, Lynch indicated the evaluation of Kaepernick's future with the franchise would take into account a little bit of everything.

"It will be a football decision, but I think part of that, there's different layers to that," Lynch said. "So I think everything will be included in the decision. I'm not talking specifically about his stance, though. I think you have a quarterback; the great ones are leaders of men, so I think all of those things will be taken into account."

The Niners originally selected Kaepernick in the second round of the 2011 NFL draft out of Nevada. He played in 69 regular-season games, throwing for 12,271 yards with 72 touchdowns and 30 interceptions while completing 59.8 percent of his passes. The 49ers were 28-30 in his regular-season starts and 4-2 with an NFC championship in his six postseason starts.

San Francisco nearly traded Kaepernick to the Denver Broncos last offseason. That deal did not happen when the Broncos and Kaepernick couldn't come to terms on a new contract.

Now, Kaepernick will enter his first trip to free agency with an uncertain market and new representation. Kaepernick had agent Jeff Nalley of Select Sports Group represent him for the reworked deal he did in October and he officially parted ways with XAM Sports after the season.