The report appears to contradict head coach Chip Kelly's comments earlier on Thursday that appeared to confirm that Kaepernick would be with the 49ers in 2016.
With the 49ers apparently intent on giving Kaepernick another shot to cement his position as the franchise's starting quarterback, the move to request a trade appears to indicate he is set on exploring his options.
Kaepernick has five years remaining on his contract signed in 2014, but with its team-friendly structure - the deal essentially allows the 49ers to move on from him after each year with little financial impact - there could be several suitors for the quarterback's services.
Kaepernick was benched in favor of Blaine Gabbert after a disastrous 2015 season, but it was expected that he would remain in San Francisco because of the natural partnership with the offensive-minded Kelly.
His $11.9-million salary for 2016 becomes fully guaranteed on April 1.