The Miami-Dade County State Attorney's office said there was insufficient evidence that any crime was committed in a room in April, when a woman said she did not know how she ended up in a hospital after having drinks with Kaepernick and 49ers wide receiver Quinton Patton and Seattle Seahawks wide receiver Ricardo Lockette at an apartment they shared in Miami.
Patton and Lockette were also investigated in the "suspicious incident," as authorities first called it, and also will not be charged.
"No charges, no indication that a criminal act was committed," said Ed Griffith of the State Attorney's office. "She was alleging that she may have been the victim of a sexual assault, and there was no evidence."
Kaepernick had said he committed no crime.
Earlier this month, the 49ers signed him to a six-year contract extension that could be worth up to $126 million. The deal also includes $12.328 million in guaranteed money. Last season, Kaepernick completed 58.4 percent of his passes for 3,197 yards with 21 touchdowns and eight interceptions, in leading the 49ers to the NFC Championship Game for the third straight season.