Yes. (I´m a teacher).
Also in some cultures it´s more usual. In Spain where we live now there are hundreds of thousands of girls called Maria + other name (Carmen, Eugenia, Isabel, Teresa, Victoria...and more) and it´s natural to call them by, and assume they are known as, the second name.
For foreigners with the concept of middle names it can lead to odd situations, e.g. at the doctor´s surgery where you don´t react to them calling your middle name repeatedly.
Most school enrollment forms ask for the child´s passport name and the name they like to be known by. It is unusual that yours doesn´t have this - I´d just write it underneath or at the side, clearly.
I know some East Asian children who have an Asian name and a more western sounding name they prefer to use, as well as of course all of the kids who prefer to be "Charlie", "Jack", "Lola", "Sam", instead of their christened name.