The African rock python, between 3.5 and 4.5 metres in length, got out of its enclosure at Reptile Ocean pet shop and slithered up a ventilation duct to the apartment above the store where the boys were sleeping.
The bodies of the two boys were discovered early the next morning, and police arrived shortly after.
Jean-Claude Savoie, owner of the store in northern New Brunswick called the incident tragic.
Savoie said the two children are the kids of his best friend and they often sleep over in his apartment. It's believed the boys lived in the building next to the shop.
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"I feel like they're my kids," he said.
Savoie said he went into the living room, where the kids were sleeping, and discovered a gruesome sight.
"I thought they were sleeping until I [saw] the hole in the ceiling. I turned the lights on and I [saw] this horrific scene," he said.
"I found the snake. It was in a hole underneath. I pinned him down and put him in a cage and the Society for the Prevention of Cruelty to Animals (SPCA) took him," Savoie said.
Savoie said the 45 kilogramme python is not normally handled by anyone, including the two children.