Marshon Sanders' mother wrote in an email to ABC7 news' sister station WLS in Chicago that there were others dressed up as Mormons, priests and Moses without incident.
Angenetta Frison said her son was forced to take his costume off. She said the school did not give her a reason.
The mother said she has taught her son to respect great people that and Jesus Christ is a great figure, adding there was nothing provocative or demeaning about the costume.
Sanders' mother said some teachers found the costume offensive. Her son was readmitted to school after changing, she said.
Sanders' costume included a long, white robe; red sash, head scarf and cross necklace.
Frison said she didn't question her son's choice of costume when he left for school.
"I encouraged him to dress as someone inspiring or uplifting," she said.
But school policy states that costumes that "could be offensive or perpetuate a stereotype of someone's culture, gender, sexual orientation, heritage or religion are not permitted."
Melinda Vajdic, school spokeswoman, said the costume could be interpreted as poking fun or perpetuating a "religious stereotype."
"Costumes trivialize," Vajdic said. "I'm sure that wasn't his intent, but we want to maintain a culture of mutual respect."
Frison and her son are members of Jesus Name Apostolic Church in Waukegan. He also attends Willow Creek Community Church in Barrington.
Last Halloween, Sanders dressed as the rap artist formerly known as Snoop Dogg.
"They didn't have a problem with that," Frison said.
The Sun-Times Media Wire contributed to this report.