Initially investigators questioned a person of interest, who was charged late Saturday night. The 35-year-old woman is accused of first-degree murder in the boy's death.
In the early hours of Saturday morning emergency crews responded to a report of an injured child in the 400 block of Avenue R South.
The boy was pronounced dead at the scene. Police said he was suffering from a fatal injury, and while they know the cause of death no details have been released.
"It’s hard for our officers to deal with. I can’t imagine what it is like for the family," said Alyson Edwards with the Saskatoon police at a press conference on Saturday afternoon. “Any type of homicide is tragic, but when you’re dealing with a small child, five years old, it’s awful."
Police said three people, who were related to each other, were also in the home when officers arrived.
The names of the accused, and of the victim have not been released. It's not clear if there is any prior connection between the two.
An autopsy will be conducted as early as Monday.
This is Saskatoon's first homicide of 2014.