Eight other children, including the victim's 7-year-old sister, were on the bus but were not harmed. Authorities took the children and the bus driver to a police station to be interviewed.
The victim, who has not been identified, attended charter middle school Palm Glades Preparatory Academy. The victim's sister went to nearby Summerville Advantage Academy.
Concerned parents gathered at the shooting site, which was cordoned off by crime scene tape as authorities combed the bus for evidence and gathered children's backpacks and belongings. The shooting occurred about seven minutes away from the school.
Fabian Otero said he was relieved his son Christian, an eighth-grader at Palm Glades, rode to school with his wife. He said he and his wife have been shaken by the killing and are going to discuss enrolling their son in a different school or possibly homeschooling him.
"I was stunned! I was stunned!" he said. "That hits really close to home. That's just scary."
About a dozen parents picked up their children early, said Lynn Norman-Teck, a spokeswoman for Florida Consortium of Public Charter School. Only a throng of TV news crews camped outside signaled the violence from earlier in the morning.
The school principal walked through every classroom shortly after hearing about the shooting to make sure the students were safe.
The school bus was not equipped with video surveillance equipment.
A phone message left for the private school bus company was not immediately returned.