Edinburg Consolidated Independent School District officials said the teen was arrested in Harris County within hours of sending a threatening email last Thursday to the assistant principal of Robert Vela High School.
According to police, the email included the words "shoot" and "shooting."
The school later contacted the police, who got the FBI involved.
ECISD Chief of Police Ricardo Perez said the FBI tracked down the teen in Harris County's Cy-Fair community and arrested him.
The juvenile is facing felony charges for making a terroristic threat and will be prosecuted in Harris County, officials said.
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