The RCMP said in a release Tuesday that a charge against Jean Claude Savoie, 38, was laid in provincial court on Monday in Campbellton, N.B.
Four-year-old Noah Barthe and his six-year-old brother Connor were found dead on Aug. 5, 2013, after an African rock python escaped its enclosure inside Savoie's apartment in Campbellton, where they were staying for a sleepover.
The RCMP alleged at the time that the 45-kilogram snake escaped a glass tank through a vent and slithered through a ventilation pipe, but its weight caused the pipe to collapse and it fell into the living room where the boys were sleeping.
Police say autopsies determined the boys died from asphyxiation.
Savoie was arrested Feb. 5 in Montreal, where he now lives, and is due in Campbellton provincial court on April 27 to face the charge.
At the time of Savoie's arrest, his lawyer Leslie Matchim said he was previously told by the lead RCMP investigator that there would be no charges against his client.
But police said the investigation continued and was eventually turned over to the Crown to determine whether charges were warranted.
A conviction of criminal negligence causing death carries a maximum life sentence.
Following the deaths of the two brothers wildlife officers removed animals from Reptile Ocean, an exotic pet store beneath Savoie's apartment. Twenty-three reptiles that are banned in the province without a permit were seized and four alligators were euthanized.
Matchim said the Department of Natural Resources decided against laying charges after conducting an investigation.
African rock pythons have been banned in New Brunswick to all but accredited zoos since 1992. Those zoos must obtain a permit in order to keep the animals.