Harbaugh said that Kaepernick visits the gym in North Miami Beach most mornings and that the player has a unique routine that ensures his whole body is in top shape for the season ahead.
"He's in there at 6.30am working out," the 49ers' official website quotes Harbaugh as saying. "His car's the first one in the lot and he knocks that out before the sun comes up.
"Colin's just a big person. If he were ever to stand next to you or me, it just illustrates how big he is. He's just a big man.
"I've seen him train. This is not a guy that's repping out as many reps on the bench as he can. This is high-tech new age kind of working on all the little tiny muscles. They know what they're doing."
Kaepernick has spent all three seasons of his career to date in San Francisco.