Kaepernick has impressed since becoming the Niners' starting quarterback, leading the team to the Super Bowl in 2012 and the NFC championship game last year.
"I really expect that real breakout year for Colin. He just has the look and feel that he's going to break out, more so than he already has. I'm really excited about everything about his game right now," Harbaugh told reporters.
"I feel like we have a lot of firepower in our corner. I feel like we have a lot of ammunition in our camp. I was just thinking about it the other day, 'It doesn't get better than this.'"
Kaepernick, who was chosen in the second round of the 2011 Draft, started every match for the 49ers last season, throwing for 3,197 yards and 21 touchdowns.