Police inspector Flavio Simao says Lucas Neiva's mother filed a complaint against the private Cidade Jardim Cumbica School in the Sao Paulo suburb of Guarulhos, saying she was told her son's hairstyle "did not conform to school standards."
The mother refused the school's request that she cut her son's hair. When she tried to enroll him for the 2014 school term, she was told there was no room for him.
The school's administration office said no one was available to comment.
Racism is illegal in ethnically diverse Brazil, punishable by up to five years in prison.