He has been charged with first-degree murder as a juvenile.
According to police, the boy shot neighbour McKayla Dyer on Saturday evening after she refused to let him see her puppy.
Her mother Latasha said that the two children attended the same school in White Pine, about 200 miles east of Nashville.
She said the family had had trouble with the boy when they first moved to the area.
“He was making fun of her, calling her names, just being mean to her. I had to go to the principal about him and he quit for a while and then all of a sudden yesterday he shot her,” Ms Dyer said.
She added: “She was a precious little girl. She was mommy’s girl. No matter how bad a mood you were in, she could always make you smile.
“I want her back in my arms.”
The Gun Violence Archive, a not-for-profit American organisation that compiles data on gun violence, says 559 children aged 11 or under have been killed or injured in the US in gun violence so far this year.
The boy shot the girl from inside his home with his father’s 12-gauge shotgun, said Jefferson County Sheriff Bud McCoig.
McKayla was taken to a nearby hospital where she later died.
Neighbour Chastity Arwood told reporters that she heard the shot ring out and saw McKayla lying on the grass.
“Trying to comfort her mama and her aunt and her grandma and her grandpa and her sister and her brother was the hardest thing I ever had to do,” Ms Arwood said.
The boy, whose identity has not been released since he is a juvenile, is expected to appear in court again on 28 October.
The shooting took place only two days after a mass shooting at an Oregon college in which nine people were killed.