The boy told investigators last month that he saw a tall man with gray hair flee the family's home and then found his sister bleeding from stab wounds.
The death set off an intense manhunt in the rural community where some residents had moved to escape big city crime.
Justin Fowler said the family was having a hard time coping with what is now a double tragedy.
"We're just trying to stay positive, but it's hard," he said.
The AP is withholding the name of the boy because he is a juvenile.
Days after his sister's killing, the boy appeared at a vigil for her. His brother Justin was photographed with the name "Leila" written on his forearm. The boy's father Barney Fowler attended with his fiancé Krystal Walters.
People across the mountain community were relieved there had been an arrest and that the crime did not appear to be the work of an intruder.
Investigators initially maintained the boy was being questioned only as a witness.
On Monday counselors were talking to students at Toyon Middle School.
"Our kids are experiencing a lot of mixed emotions," said school Superintendent Mark Campbell. "We have a degree of ease that it's not a random assailant, but it's a double whammy from our school perspective. We lost a student and we stand to lose another. It's a lot for our kids to process."
On Friday, as speculation built that perhaps the boy was involved, his biological mother, Priscilla Rodriguez, told Sacramento television station KOVR her son "could never hurt his sister."