The RCMP confirmed Friday that the child died in an Edmonton hospital.
"Our prayers and thoughts are with her family, friends and the community of St. Paul," the Mounties said in a release.
The Grade 6 girl's identity is not being released.
Police have charged Richard Edward Benson with dangerous driving causing bodily harm, resisting arrested and possessing a controlled substance.
They allege Benson, 46, was behind the wheel of the van when it smashed into a French class in the basement of Racette Junior High School in St. Paul on Thursday shortly after the morning bell.
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The two other badly hurt girls remain in hospital.Ralph Benson says his brother, Richard, was on prescribed medication and sometimes smoked marijuana to alleviate pain from ongoing health problems. He says his brother was the victim of a severe beating more than a decade ago that put him in a coma and left him with a metal plate in his head.
"People don't realize what he has gone through and his medical condition and I don't know — I just believe he shouldn't be locked up in a jail cell right now. He should be in the hospital," Ralph Benson told The Canadian Press in an interview.
"We're all praying for the children, too," he said. "We all have children, too, and we all feel horrible also."
He said his brother is a single father of nine who lives on the outskirts of St. Paul. Only two of his kids live at home and he had just dropped them off at school before the crash.
He said Richard hasn't been able to work since the beating and was surviving on government assistance for the severely disabled. He said his brother had to undergo a series of medical clearances before he got his driver's licence back several years ago. The family was concerned about him driving, but he was happy.
"He felt that he had his life back because he could drive his kids to school and stuff and that he was doing OK," Ralph Benson said. "You have to give the guy the benefit of the doubt, I guess."
Ralph Benson said an ambulance was called to the home several times in the last few months because of his brother's seizures. The last one the family knew of was on Sunday.
RCMP Chief Supt. Randy McGinnis said the driver of the van was initially combative with police after the crash.
"Yesterday he was resistant ... but I can say this morning he was very remorseful, very apologetic (about) what has transpired and co-operated fully with our investigation," McGinnis said at a news conference.
McGinnis said police are waiting on toxicology tests taken after the driver was arrested.
"We have not charged him with any impairment offences, but we are still waiting for analyses on the blood that we have been able to obtain," he said.
Richard Benson has a record, McGinnis said, but the officer added it "might be dated."
McGinnis described the concern of the fire chief and police officers when they arrived at the crash scene.
"There was a huge issue with safety because this vehicle came to rest on the desks in the classroom and there was great fear that the vehicle may have tipped, come off the desks and then land right straight on top of the students that were still underneath, or place more vehicle weight upon them," McGinnis said.
"There was considerable confusion and frustration in dealing with that and trying to make sure that the scene was secured to get those students out."
The RCMP have yet to determine how fast the minivan was going. McGinnis said that information will come from computer modules, if the van was equipped with them, or from analysis of the scene.
But he pointed out that conditions were deteriorating at the time because it was snowing, so "we may not be able to determine the speed from the evidence left at the scene itself."
Alberta Education Minister Jeff Johnson thanked the school board trustees and staff for their courage and the emergency responders who arrived on the scene.
"I also want to acknowledge the impact this tragic event has had on the students and entire community," he said.
“On behalf of my colleagues, my thoughts and prayers are with the entire community during this difficult time. The loss of a young life is devastating," he added.A bail hearing for Benson is to be held Monday in St. Paul.
McGinnis said Benson wasn't seriously hurt.
The school was closed Friday.