The uniform policy of Melton Christian School in Melbourne prohibits non-Christian head coverings for boys.
But the boy's father, Sagardeep Singh Arora, argued that not letting him wear the patka, a child's turban, was indirect discrimination.
The tribunal ruled in Mr Arora's favour on Tuesday.
Having uncut hair, or kesh, is a Sikh belief and wearing a patka is an essential practice of the religion.
But the Christian school chose not to make an exception for the boy, Sidhak, after an enrolment meeting with the family last year.
