The boy died in December 2012, three days after police say they were called about a child in medical distress at a rural property near Garrick, a hamlet 230 kilometres northeast of Saskatoon.
Police say the child was taken to Nipawin for medical treatment, but couldn't be airlifted to Saskatoon because of freezing rain that night.
They say he was transported to Saskatoon eventually, but died there in hospital on Dec. 7.
Sgt. Craig Cleary says the coroner reported the death was caused by blunt force trauma.
The suspect, Shane Pashke, 33, of Garrick faces a charge of second-degree murder.
He is scheduled to appear in court in Melfort on Monday morning to face the allegation against him.
Cleary says police are not releasing the child's identity until they see if a publication ban is requested in court.
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