Updated

Santa Clara, CA (SportsNetwork.com) - What a difference a few years make.

Colin Kaepernick, a backup two seasons ago, now has the money to prove he's developed into one of the NFL's top quarterbacks.

The San Francisco 49ers made Kaepernick their franchise quarterback Wednesday, signing him to a six-year contract extension through the 2020 season.

The deal will pay Kaepernick up to $126 million, with $61 million guaranteed, according to NFL.com. The final year of his rookie contract was to pay him less than $1 million.

"Colin's hard work and dedication have played an integral role in the recent success of the 49ers organization," said general manager Trent Baalke. "His work ethic, leadership and on-field production have positively influenced our team, and we look forward to his continued growth in all areas.

"Our organization always looks to reward our players for their contributions and commitment to the team."

Last season, Kaepernick set career highs in completions (243), passing yards (3,197) and passing touchdowns (21), while also recording 92 rushing attempts for 524 yards and four touchdowns. It was his first full season as a starter.

He led the 49ers to a 12-4 record and a berth in a third straight NFC title game.

In 2012, Kaepernick played in 13 regular-season games (seven starts) and threw for 1,814 yards with 10 touchdowns and three interceptions. He carried the ball 63 times for 415 yards and five scores.

Kaepernick then earned national attention in his first career playoff start by setting the NFL single-game rushing record by a quarterback with 181 yards against Green Bay in the divisional round. The 49ers eventually lost to the Ravens in Super Bowl XLVII.

"I'm trying to win as many Super Bowls as I can," Kaepernick said. "That's not necessarily realistic to win it every single year, but that's what your goal is."

Picked in the second round of the 2011 NFL Draft by San Francisco, Kaepernick has played in 32 games (23 starts), completing 382-of-639 passes for 5,046 yards, 31 touchdowns and 11 interceptions.