Authorities charged the older boy as a juvenile delinquent Monday. Children must be at least 13 years or older to be prosecuted for murder in New York.
State police on Tuesday declined to reveal what was behind the gunfire.
Police say the boys were home alone late Saturday afternoon when the older brother took a rifle from inside the house and fired a single shot, mortally wounding his brother.
State police did not identify the children because of their ages, but a neighbor says the victim was Daniel Schaeffer. No one answered the telephone Tuesday at the family's house in Deposit, 30 miles east of Binghamton.