"We have registered one dead and I think it's the final number," said Lenka Ptackova, a spokeswoman for the regional emergency service.
Earlier it was reported that it was the driver who had been killed.
Ptackova said the girl who died was "aged 17-20 years, according to estimates from the site", she said.
A further 41 people were injured.
"The bus was full of French kids. Some of the injured were taken to hospital by helicopters," said Pavla Jakoubkova, spokeswoman for the local fire brigade.
Ptackova said all the passengers had been taken to hospital with injuries ranging from light to serious. Most of the passengers were youths aged 10-18, according to rescuers.
The accident occurred after 5.30am local time near Rokycany, about 80 km west of the Czech capital Prague.
"The bus skidded off the motorway, crossed a field, broke a few trees and fell across another road and finally crashed into a slope," said Jakoubkova.
Pictures in Czech media disclosed the bus belonged to Champagne Mobilites, a unit of French transport group RATP. Champagne Mobilites offers transport in the Marne and Ardennes regions, according to its website.
Police spokeswoman Martina Korandova said the police were investigating the possible cause of the accident.
She declined to give details about the bus or where it was heading, citing a Czech law protecting personal information. The French embassy said after the accident that it had no details to give either.