The snake is believed to have escaped from the Reptile Ocean store and made its way into the apartment, where the boys, ages 5 and 7, were visiting a friend, the Canadian Broadcasting Corp. reported.
"Police are investigating two sudden deaths of two young boys," Constable Julie Rogers-Marsh said, adding it appears the snake got into the building's ventilation system.
"It's believed the two boys were strangled by the snake," she said. Autopsies were scheduled for Tuesday in Saint John.
"This is a tragedy," Deputy Mayor Ian Comeau said. "The city is in shock."