If you are in the U.S., you have a right to be treated as your identified gender. Please speak up for yourself, either to a counselor, and if that doesn't work, to an administrator. It would help if you had a parent or some other non-student ally on your side. But you are in the right. Your school administrators may be ignorant about their responsibility to accommodate you, and you may have to be the one who educates them.
If necessary, seek help from an LGBT support organization. Is there a PFLAG chapter near you? If not, consider contacting Lambda Legal or one of the other national organizations.
Please don't let this go. They are required to treat you reasonably.