Now, whether Kaepernick receives that money as a member of the San Francisco 49ers or with a different team that might acquire the quarterback in a trade remains to be seen.
Kaepernick still could make less money from any acquiring team should he agree to a pay cut as part of the deal. It had been reported that Kaepernick's salary would not become guaranteed until Friday, but with the league day ending at 4 p.m. ET, the calendar flips to the next day -- hence the contract status changing Thursday.
ESPN's Adam Schefter reports that Kaepernick is expected to remain with the 49ers past Friday, but trade talks regarding the quarterback are expected to continue up to and throughout the NFL draft on April 28-30.
The Super Bowl champion Denver Broncos, who lost Peyton Manning to retirement and Brock Osweiler to the Houston Texans in free agency, have long been linked to Kaepernick, reportedly envisioning him competing with the recently acquired Mark Sanchez. But a restructured Kaepernick contract would seemingly be a necessity to any trade with Denver.
Entering Thursday, the Broncos had less than $2.9 million available in salary cap space, which ranked 28th of the 32 teams in the NFL. The Niners, meanwhile, had the second-most cap space in the league at more than $53 million.
Recent reports had the Broncos valuing Kaepernick as a fourth-rounder in a trade. Denver, though, does not have a fourth-round pick that can be traded in this year's draft after sending its original selection that round to the Baltimore Ravens last year in a trade for center Gino Gradkowski.
A second-round draft pick of the 49ers out of Nevada in 2011, Kaepernick became San Francisco's starter midway through the 2012 season. He was the starting quarterback as they advanced to the Super Bowl that season, as well as the following year, when they advanced to the NFC title game. But after regressing in 2014 under coach Jim Harbaugh, Kaepernick hit rock bottom in 2015, getting benched by coach Jim Tomsula in favor of Blaine Gabbert after a 2-6 start.
This offseason, with Kaepernick recovering from surgeries to his left (non-throwing) shoulder, right thumb and left knee, his agents asked the 49ers for permission to explore potential trades.
"But our intent was for him to be back and to go to work ... the more important thing is what our expectations are of the player," general manager Trent Baalke said. "He's under contract, and unless -- or until that changes -- our expectations don't change."
Permission being granted should not be taken as a sign that the Niners want to move on from Kaepernick, Baalke has said.
"Because I think sometimes it helps players ... it gives them a chance to see what their options really are," Baalke said. "And it also gives us a chance to say, 'We didn't hold you back from doing anything.' This is new for everybody.
"Obviously, coach [Chip] Kelly would love to work with him and feels he could fit into the system that coach has, and go to work. I think that's the main purpose of it."
Kelly, who was hired in January, said he has heard nothing negative from Kaepernick and said he has not tried to sway him to stick around Santa Clara.
Will the 49ers still trade Kaepernick?
Adam Caplan discusses the likelihood that 49ers QB Colin Kaepernick will be traded around the time of the NFL draft.