The boy, whose name was not released, was taken into custody at a Calaveras County Sheriff's Office substation in his hometown of Valley Springs shortly after 5 p.m. PDT, Sheriff Gary Kuntz said.
Leila had been found stabbed in the family's home April 27. She and her brother had been alone at the time and had told investigators he had seen an intruder, sending authorities in search of a 6-foot-tall white or Hispanic male with a muscular build.
"Citizens of Calaveras County can sleep a little better tonight," Kuntz said following the boy's arrest on a homicide charge.
"We are devastated," the girl's mother, Crystal Walters, told CNN via her Facebook page. "She didn't deserve this. ... She was so full of life."