Law enforcement officials said they discovered the teen's body late Monday night at the family home in rural White Springs in north Florida.
The 15-year-old's sister, age 11, assisted in the shooting but didn't pull the trigger, sheriff's spokesman Murray Smith said. The older girl got the gun from a room that her parents had locked, Smith said.
But a motive for the shooting, in the town of fewer than 800 people on the banks of the Suwannee River, remained unclear Tuesday. "There's no real rhyme or reason to it," Smith told The Gainesville Sun.
White Springs police said they began looking for the girls late Monday night after they received a phone call from the mother of a friend of the younger sister. The friend had received a "weird phone call" from the girl, saying she had run away and needed someone to pick her up from a Dollar General store, according to a police report. When the woman arrived, she found the older sister there, too.
The older girl remarked that something might have been wrong with another sibling at home, officers Brad Meeks and Joseph Dyess noted in their report. The teen told the officers that her parents were not expected home until 5 a.m. Tuesday.
As she spoke, she applied makeup and "would not maintain eye contact and appeared emotionless," the officers wrote.
But soon she started crying and told the officers that her brother had beaten her, thrown her into her bedroom, and locked the door. She told officers that when he went to sleep, her younger sister unlocked the door. The teen said she then shot her brother, according to the report.
The officers contacted the Columbia County Sheriff's Office to check the house. The teen told authorities the weapon was on a blanket in the hallway. Deputies found the brother dead in the living room.
A younger sibling, age 3, also was in the home at the time and is now in state custody. The agency is working with deputies to determine what happened and to help the surviving siblings, Department of Children and Families spokesman John Harrell told the newspaper. He said state law prohibited him from releasing details of any past incidents the family might have had with the department.
The parents were charged with child neglect and are accused of failing to supervise in the treatment of children, Smith said. He said the father is a truck driver and the mother had left with him on a trip. The home did not have a recent history of visits from the sheriff's office, Smith said.
Third Circuit State Attorney Jeff Siegmeister told the newspaper that he hasn't decided whether to charge the girls as adults. Because of the suspects' ages, The Associated Press is not naming the girls, their brother or the parents.
Children arrested for crimes and treated as juveniles can be held in detention for a maximum of 30 days.
"Sometimes we can send them home after that, but in light of all of the facts in this case, we don't have any place to send the children," Siegmeister told The Sun. "I may be forced to actually charge them as adults to hold them in juvenile detention until I can work something out. I don't know all of the facts yet."