Start by working with her teacher.  You may need to go in someday after school and tour the bathroom with her to allay fears.  Get familiar with the furniture of the school bathroom and remind her of similarities to home.  Start simply by washing hands in the sink.  Remind her she will have some privacy but that the teacher or teacher's aid will watch out for all students using the room with permission.  Talk about why she is concerned.  Perhaps it is other children using it at the same time.  Some kindergarten bathrooms are small and some are shared.  Be clear as to what you need to dispel.

Wayne Yankus, MD, FAAP
expert panelist: pediatrics