I'm going to the be the first one to say that I don't understand exactly why this exercise is done or why it seems to be do popular in the weight room.
To do a high knee step up, place one foot on a box that puts you at parallel or below. Make sure that your entire foot is on the box. From this position, keep your head and chest up and your lower back arched, and step onto the box. Now, here is where it gets strange. After you do the step up, take the opposite leg (the one NOT on the box) and drive your knee up.
I think my mom does these in aerobics class.