Kaepernick has led the 49ers to two straight NFC Championship games and one Super Bowl appearance in his more than two seasons as a starter. Last season, Kaepernick passed for 3,197 yards with 21 touchdowns and eight interceptions and also ran for 524 yards and four touchdowns.
"The priority is that Colin Kaepernick is a San Francisco 49er for however long we can have him be a San Francisco 49er," Harbaugh said via NFL.com. "It's definitely a high priority."
Kaepernick, 26, expected to make $973,766 next season before entering free agency in 2015.
"I'll give you an anecdote," Harbaugh said. "There's really no one that can compete with him in a workout situation. He will bury everybody. And when someone tries to compete with him, he just ramps his competitiveness up. And then someone is over on a knee throwing up. He's unbelievable."