A male student was in custody but authorities did not release his name or age and said they are still interviewing him. A gun was also recovered at the scene in Homestead, south of Miami, but authorities didn't say where or how many times the victim was shot.
"We still don't know what the motive may have been," said police spokesman Det. Alvaro Zabaleta.
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.
Grief counselors were on their way, but the school was relatively calm as most of the students had not yet heard about the shooting. 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.