PROFESSIONAL CAREER

2011 season

On April 29, 2011, the San Francisco 49ers traded up with the Denver Broncos from the thirteenth pick in the second round (45th overall) to select Kaepernick as the fourth pick in the second round (36th overall) at the 2011 NFL Draft. The Broncos received picks 45, 108, and 141 overall in exchange for the 36th overall pick.Kaepernick spent the 2011 season as backup to Alex Smith and attempted just five passes during the season.

2012 season

In 2012, Kaepernick was initially used sparingly to run certain plays. He scored his first career touchdown in the team's fourth game when he scored on a seven-yard run against the New York Jets. In Week 10, against the St. Louis Rams, Kaepernick replaced Smith in the second half of the game after he suffered a concussion in the first half. Kaepernick completed eleven of seventeen passes for 117 yards and added 66 rushing yards and a rushing touchdown as the 49ers and the Rams ended the game in a 24–24 tie. He got his first NFL start the next game on November 19, during a Monday Night Football game against the Chicago Bears at Candlestick Park. Kaepernick completed 16-of-23 for 246 yards with two touchdowns in a 32–7 win against a highly ranked Bears defense. A quarterback controversy began. Smith was ranked third in the NFL in passer rating (104.1), led the league in completion percentage (70%), and had been 19–5–1 as a starter under Harbaugh, while Kaepernick was considered more dynamic with his scrambling ability and arm strength. Smith was cleared to play the day before the following game, but Harbaugh chose not to rush him back and again started Kaepernick. He remained the starter for the rest of the season and led the 49ers to an 11–4–1 record and a berth in the NFL playoffs.

In his first career postseason start, against the Green Bay Packers, Kaepernick had 263 passing yards, two passing touchdowns, one interception and 181 rushing yards and two rushing touchdowns as the 49ers defeated the Packers 45–31. With his performance, he set an NFL single-game record for most rushing yards by a quarterback with 181, breaking Michael Vick's record of 173 in a 2002 regular season game. He also broke the 49ers postseason rushing record, regardless of position and joined Jay Cutler and Otto Graham in both as the only players in NFL history to run for two touchdowns and pass for two others in a playoff game. In the NFC Championship, the 49ers defeated the Atlanta Falcons 28–24 with Kaepernick completing 16-of-21 passes for 233 yards and one touchdown. The team advanced to Super Bowl XLVII in New Orleans against the Baltimore Ravens. Kaepernick threw for 302 yards, one passing touchdown, and ran for a touchdown, but the 49ers fell behind early and could not come back, losing by a score of 31–34.

2013 season

KIn the season opener of the 2013 season against the Green Bay Packers, Kaepernick threw for a career-high 412 yards and three touchdowns, the first 400-yard game by a 49ers quarterback since Tim Rattay on October 10, 2004. Kaepernick ended the season with 3,197 yards passing, 21 touchdowns, and eight interceptions, 524 yards rushing yards and four rushing touchdowns and led the 49ers to a 12–4 record and a berth in the NFL playoffs.

In the Wild Card Round, the 49ers played the Green Bay Packers. Kaepernick had 227 passing yards, one passing touchdown, one interception and added 98 rushing yards as the 49ers beat the Packers 23–20. In the divisional round, against the Carolina Panthers, Kaepernick had 196 passing yards, one passing touchdown, 15 rushing yards, and one rushing touchdown as the 49ers beat the Panthers 23–10. In the NFC Championship Game, against eventual Super Bowl champion Seattle Seahawks, Kaepernick had 153 passing yards, one passing touchdown, two interceptions and rushed for 130 yards as the 49ers lost to the Seahawks 17–23, ending the 49ers' season and attempt to return to the Super Bowl.

2014 season

On June 4, Kaepernick signed a six-year contract extension with the 49ers, worth up to $126 million, including $54 million in potential guarantees, and $13 million fully guaranteed. On September 17, Kaepernick was fined by the NFL for using inappropriate language on the field. On October 9, he was fined $10,000 by the NFL for appearing at a post-game press conference wearing headphones from Beats by Dre, while the league's headphone sponsor was Bose. In a game against the San Diego Chargers, he ran for a 90-yard touchdown. The 49ers finished the season 8–8 and failed to make the playoffs for the first time since 2010. Kaepernick threw for 3,369 yards with 18 touchdowns and 10 interceptions. He rushed for 639 yards and one touchdown. Following the season, head coach Jim Harbaugh left to coach the University of Michigan.

2015 season

In 2015, Kaepernick struggled under new head coach Jim Tomsula. A day after a 27–6 collapse at St. Louis in Week 8, Kaepernick lost his starting job to backup Blaine Gabbert for Week 9 against Atlanta. With Gabbert starting as their new quarterback, the 49ers narrowly won 17–16. On November 21, the 49ers announced that Kaepernick would miss the rest of the season because of an injured left shoulder that required surgery. He ended the season with 1,615 yards passing, six passing touchdowns, five interceptions and 256 rushing yards with one rushing touchdown in nine games. Head coach Tomsula was fired following the season and the 49ers hired Chip Kelly as his replacement. In February 2016, Kaepernick expressed an interest in being traded.

2016 season

Kaepernick was coming off three surgeries entering the 2016 season, needing operations on his thumb and knee in addition to the season-ending shoulder procedure. After having lost weight and muscle mass because of the injuries, he competed for the starting quarterback position with Gabbert. Kelly named Gabbert as the starter to open the season. Prior to the 49ers Week 6 game against the Buffalo Bills, Kelly announced Kaepernick would start, marking his first start of the season. On October 13, it was announced that he and the 49ers restructured his contract, turning it into a two-year deal with a player option for the next season. He completed 13-of-29 passes, with 187 passing yards, one passing touchdown and 66 rushing yards in the 49ers 45–16 loss to the Buffalo Bills. On November 27, he recorded 296 passing yards, three passing touchdowns and 113 yards rushing in the 49ers' 24–31 loss to the Miami Dolphins. He joined Michael Vick, Cam Newton, Randall Cunningham, and Marcus Mariota as the only quarterbacks in NFL history to record at least three passing touchdowns and 100 yards rushing in a game. In a Week 13 loss to the Chicago Bears, Kaepernick threw a career-low four yards before getting benched for Gabbert. He returned to the starting lineup the following week and threw for 183 yards and two touchdowns in the 49ers' 13–41 loss to the Atlanta Falcons. On December 24, Kaepernick recorded 281 total yards, two passing touchdowns, one interception, one rushing touchdown, and a two-point conversion on the game-winning drive as the 49ers beat the Los Angeles Rams 22–21 to get their first victory on the season with Kaepernick as the starter. For the 2016 NFL season, Kaepernick played twelve games and ended the season with 2,241 passing yards, sixteen passing touchdowns, four interceptions and added 468 rushing yards and two rushing touchdowns.

During the offseason, San Francisco hired Kyle Shanahan from Atlanta to be their new coach. He planned to run the same offense which he ran the previous year with the Falcons, and did not believe that Kaepernick fit the scheme. The 49ers told Kaepernick that they planned to release him. On March 3, 2017, he opted out of his contract and became a free agent at the start of the 2017 league year on March 9.