Bath - to add - I was a noncatholic in a catholic primary school. You couldn't take communion until I think it was year 3 when you did 1st holy communion. Some teachers dealt with kids not having communion well and some didn't .

The two extremes of my experience were as follows:
the bad extreme was being excluded from class in year 3 while the majority of the class had "lessons" on how to take first communion - being excluded meant sitting on the steps outside the classroom with two other kids and being told not to move. This same teacher used to make the non catholics sit in the back of the church away from the rest of class (we didn't care - we used to play games and noone would notice).

The good one was where I was given jobs to do in church instead. For two years I was in charge of the overhead projector that had the hymn/song words on it and I had to turn it on and move the overhead if it was a long one and then turn it off. It made me feel included in the proceedings and didn't draw attention to the fact that I wasn't taking communion like most of the kids were.

If it is a concern maybe speak to the head teacher and ask how they deal with such situations.