Emergency officials were called to the scene of an accidental discharge of a firearm on Morton Street at about 11:40 a.m.
An official with the Boston Public Health Commission confirmed to FOX 25 a child was transported to Boston Medical Center.
Officials originally said the victim was 11 years old. They later corrected his age, saying he was 9.
Mayor Martin Walsh and Boston Police Commissioner William Evans held a media briefing near the scene at 12:40 p.m., during which they confirmed the child had died.
Evans said the victim's brother, 14, ran from the home after the shooting. Police believe he panicked. He and the gun were located close by at a home on Walk Hill Street.
The teen was interviewed by homicide investigators and will be arraigned next week on charges of involuntary manslaughter and unlawful possession of a firearm, officials say. Based on evidence at the scene and statements, investigators believe that the teen was handling the firearm recklessly when it was discharged.
"Part of our investigation in the days to come will be determining how this weapon got into the hands of a 14-year-old," Suffolk County District Attorney Daniel F. Conley said. "In the meantime, I want to make something crystal clear: if you know about an illegal firearm in this city, help us prevent another tragedy like this one. Boston Police are doing a tremendous job of taking guns off the street, but they aren't mind readers. They need tips and information about these weapons before they're used."
A relative told Fox 25 the 9-year-old was home sick from school Friday, but it wasn't clear if that's why the 14-year-old was home. It's not known if the two were supervised inside the home.
Neighbors are shocked by the tragic incident and believe that the boy should have been in school.
Neighbor Debra Brown said, "She didn't have to lose her baby all he needed to do was be in school."
Both Walsh and Evans expressed their condolences to the family. Walsh asked residents of Boston to call the police department if they have a gun in their home.
"Let's get these guns off the streets," he said.
State Senator Linda Dorcena Forry released the following statement Friday:
"On behalf of my constituents in the First Suffolk District, I extend my deepest sympathies to the family of the 9-year-old boy who was tragically shot to death this morning. As authorities investigate the circumstance of the shooting, my office stands ready to assist his family and neighbors in this difficult time."
Anyone with information regarding this incident is asked to call the Boston Police Homicide Unit at 617-343-4470.