The 26-year-old is entering the final year of his rookie deal in the 2014 season, but the club are hopeful that they can secure his future before he hits free agency next year.
Harbaugh told CSNBayArea.com: "The priority is Colin Kaepernick is a San Francisco 49er for however long we can have him be a San Francisco 49er. It's definitely a high priority. Amazing individual. Amazing player. He shows up and works all the time.
"There's really nobody to compete with him in a workout situation. He will bury everybody. And then when somebody tries to compete with him, he just ramps his competitiveness up and somebody's over there on a knee throwing up."
Kaepernick threw for 3,197 yards along with 21 touchdowns to eight interceptions in the 2013 season.