A Melbourne Christian school discriminated against a Sikh boy after refusing to enrol him because he wore a turban, a tribunal has ruled.

By not allowing five-year-old Sidhak to attend Melton Christian College wearing a patka, or children's turban, the school breached the Equal Opportunity Act, the Victorian Civil and Administrative Tribunal found on Tuesday.

"Whilst MCC is a Christian school, it has an open enrolment policy which means that it accepts enrolments of students from other faiths," VCAT member Julie Grainger found.

"A little over 50 per cent of the school community does not identify explicitly as Christian and many families at the school have no religious beliefs.

"It is not reasonable to accept enrolment applications from students from non-Christian faiths only on the condition that they do not look like they practice a non-Christian religion."

Sidhak's parents, Sagardeep Singh Arora and Anureet Kaur Arora, tried to enrol their son at the school in 2016 because it was close to home and where Sidhak's cousins studied.

The tribunal found the school could have amended its uniform policy to allow the child to wear a turban in school colours, and Ms Grainger ordered the parents and school negotiate an agreement on what orders could be made to resolve the situation.

"I consider that MCC's uniform policy, in so far as it prohibits head gear of a non-Christian faith, could be described as 'openly discriminatory'," the VCAT finding read.

In a statement, Sagardeep Singh Arora and various Sikh groups said "we are very pleased that religious freedom... is alive in Victoria".

The Victorian Equal Opportunity and Human Rights Commission said the decision was an important test case for exemptions to the Equal Opportunity Act.

"VCAT's decision shows that all schools must ensure their uniform policies are not discriminatory," commissioner Kristen Hilton said.

Melton Christian College , which during the hearing insisted its decision was lawful under exemptions to the Equal Opportunity Act, said it would work with the family to find "a constructive way forward".

"We had thought that we were acting in accordance with the law, and so we respect the finding of VCAT," principal David Gleeson said.