The children aged 15 and 12, were killed by the impact alongside the 49-year-old driver and a 27-year-old supervisor, according to Lisa De Wilde, a spokeswoman for the prosecutor's office.
The other five schoolchildren on the bus were injured in the crash at a railway crossing in Buggenhout, a Dutch-speaking municipality about 25 kilometers (15 miles) northwest of Brussels.
"A tragic collision between a train and a school bus took place in Buggenhout this morning. Four people have been killed, including two children," Belgium's deputy prime minister Maxime Prevot wrote on X.
Images from the scene in the Flanders region showed a badly damaged minibus lying on its side on a road next to a railway line, with tents set up by emergency workers around.
The commuter train remained halted on the tracks as forensic teams examined the site.
