A threat was originally posted Thursday night, which police investigated, but a new threat was posted around 10 a.m. on Friday, school officials said.
The juvenile was arrested Friday afternoon, and authorities said no explosives or weapons were found.
The Temecula Valley Unified School District said the threats are widely associated with the clown hoax rumors that have been ongoing this week. Classes were canceled for the day following Friday's threats.
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The school district posted on its Facebook page that the threats have caused a "disruption" and as a result, "continuing with an instructional day is not an option."
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Authorities said those behind the threat could face felony charges for making criminal threats.
Administrators were asking that parents follow pickup procedures to keep things orderly and safe.
In order for students to be released, parents must personally go to the school's gym anytime between 10:45 a.m. and 2:30 p.m. For parents authorizing students to leave campus by their own means, they must call the student on a cellphone and the student can hand the phone to a reunification staff member, who will verify the guardian's identity before releasing the student. Parents and guardians can also email the school with the same information.