The boy had told investigators that he came across an intruder in their Valley Springs home around noon April 27. He described him as a man being tall with long, gray hair. The boy said he went to check on his sister, Leila Fowler, and found she had been stabbed. The girl was later pronounced dead at a hospital.
Law enforcement warned residents of the quiet town just east of Stockton to keep their doors locked as they searched for a suspect. Authorities conducted door-to-door searches and divers also searched two nearby reservoirs.
A neighbor who told detectives she saw a man run away from the home later recanted her statement.
As part of the investigation, authorities seized knives from the home Leila shared with her father, stepmother and siblings to determine if one could have inflicted the fatal wounds.
No further details were released on how investigators determined that the boy was behind the stabbing.
A motive was not immediately known.
The Associated Press contributed to this report.