The incident allegedly happened during the bitter cold morning on Thursday.
The family in Bed-Stuy says their son, who attends pre-K at William Floyd P.S. 59, asked the teacher if he could use the bathroom around 10:00 a.m.
After he went, the family says the boy could not find his classroom, so he left school and walked home without a coat.
He only lives across the street, but the boy's father found him standing on the doorstep.
The DOE says the school referred the matter to the Special Commissioner's Office.