Police confirmed the 49-year-old man was charged with four counts of dangerous driving cause serious injury on Wednesday.
He will appear in Melbourne Magistrates Court via video link.
One child remains in intensive care and several have suffered complete or partial amputations after being severely injured in Tuesday's crash.
Ten children aged five to 11 sustained traumatic or serious injuries when the school bus carrying 45 kids collided with a truck and rolled on its side about 3.40pm on Tuesday.
The male bus driver sustained minor injuries.
A Code Brown, an emergency response for hospitals anticipating mass causalities, was declared after the accident and ran until 8pm.
Specialist doctors were called in to perform emergency surgeries at the Royal Children's Hospital after seven children were admitted and two discharged.
Students from Exford Primary School were going home when a truck hit the school bus from behind at Eynesbury, 44km west of the Melbourne CBD.
Children were trapped inside the bus before witnesses and emergency workers pulled them from the wreckage and took them to hospital.
Parents faced an anxious wait overnight before finally being reunited with their children early Wednesday morning.
The seven children are still in a serious condition, with four undergoing surgery overnight, one in intensive care and another two going into theatre on Wednesday.
Bernadette McDonald, chief executive at Melbourne's Royal Children's Hospital, said so far one child has had a complete limb amputation due to their injuries.
"The children have suffered multiple and traumatic injuries including partial and complete amputations of arms, multiple crushed limb injuries, severe lacerations to head and body, head injuries and glass shard injuries," Ms McDonald told reporters.
"Three patients are currently receiving spinal support and being monitored, carefully, in terms of spinal injuries."
Multiple surgeons are in attendance including the hospital's own doctors and vascular and specialist microplastic surgeons from Royal Melbourne Hospital.
"You would understand with these sorts of injuries very small vessels need to be repaired and reattached," Ms McDonald said.
Many of the children will need to undergo multiple surgeries in the coming days and weeks and long-term rehabilitation therapy is likely.
Ms McDonald said the situation was very traumatic.
"We have some very traumatised families and children in our hospital at the moment," she said.
"We're working extremely hard to provide that trauma support and care that they will need not just now but in the coming weeks and months."
Counsellors are going to Exford Primary School to help students process the tragedy.
Premier Daniel Andrews said he had been in contact with the school's principal Lisa Campo.
"The reason I called Lisa last night and again this morning was just to make sure that she knew and understood that 'whatever you ask for ... the answer will be yes. We're there for you'," he told reporters.
Prime minister Anthony Albanese said the crash was horrific.
"My heart goes out to them and to their families at what must be an extraordinarily difficult time," he told reporters.
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Kids Helpline 1800 55 1800 (for people aged 5 to 25)
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