Venice's Court for Minors said the boy "tries in every way to show that he is different" and described his attitude as "effeminate in a provocative way", according to local paper Mattino Padova.
A social services report said the child from Padua, northern Italy, suffered a "personality disorder" and argued that he has difficulty forming relationships due to dependence on his mother.
It also detailed an incident in which the boy wore eyeshadow and nail varnish to school, which his mother argued was for a Halloween party.
According to the court, the child's current home environment deprives him of his constitutional right to the "full development as a person".
Judges ruled that he spend 12 hours a day, from 7am to 7pm, in a 'youth community', to gain independence from his mother.
However, the lawyer representing the boy's mother, Francesco Miraglia, described the decision as "outrageous" and said he would appeal the verdict in a secondary hearing next week.
Local MP for the Democratic Party Alessandro Zan criticized the decision, writing on Facebook that he had submitted an urgent request to the government to ensure the accountability of those involved in the decision.
"When discrimination comes from those who are meant to protect us, we cannot help but wonder when and where the system of state guarantees stopped working," said Zan.