Two things are important here. First, what are the antecedents to this specific behavior? It is important to find out if there is something that triggers this behavior. Second, it is important to make sure he is occupied at all times, especially while breaking this habit. Perhaps you can give him something to hold during class, as a distraction.

I would actually make a log of when the behaviors occur. Write them down so you can attempt to find a pattern in the behavior and discover the cause of it. In the meantime, try to keep the downtime to a minimum. Have something for him to do, even during transitions! Consider having him be your teacher helper, for example, and passing out worksheets for you, helping you set up problems on the board, etc.

Unfortunately, parental cooperation is so crucial with things like this. If they allow it in the home, chances he will stop doing it in school are slim to none. Maybe a guidance counselor would be able to help with this issue? They may be able to have a talk with him. You can only help so much without the parent's cooperation since you cannot control what is going on outside of school. If it is being supplemented by him parents in a negative way, authoritative action may need to take place to stop this.

I feel that a lot of these physical behaviors can tend to happen when a child is either: distracted, concentrating, or not thinking. Giving the child an alternative behavior while they are doing these things (e.x. a stress ball) would probably be the most helpful. However, this is only me assuming things, and it is important to know exactly what may be causing this behavior. Try to notice what he is doing whenever the behavior occurs. Is he focusing? Distracted? This can help you know when you will need to redirect him.

I think that the first thing you should do in this situation is have a conference with the parents. If he is exhibiting this behavior at home and they are not addressing it then it will probably not change at school. While Andrew is working give his a fidget to keep his hands busy and out of his pants. It might also be a good idea to get a counselor involved to talk to him about what is an isn't appropriate behavior in class.

Pay attention to what is triggering this behavior. Is it a bathroom issue? a nervous thing? After the parent conference start making notes as to when it happens. I would also maybe try giving him something that is quiet for him to hold in his hand.

remind them that it can be seen as inappropriate to others in the classroom and can make them uncomfortable.

Maybe replace this behavior with a stress ball or a tennis ball.

If I were the teacher in this situation, I would try to find out what behavior or cause is making the student commit such an act, or I would write a counselor referral to see if she could get to the problem of the situation.

I think it is important to talk with the parents and try to find out the root of the cause. I believe putting Velcro or allowing the student to hold something would decrease him putting his hand in his pants. I think it is important to keep the student occupied at all times.