Police say the school received a report of a 16-year-old student making threats to harm other students on Monday.
Officers tracked down the suspect and searched his home.
Investigators discovered the boy's 35-year-old father, Jonathan Olvera, had six guns in the house, all found unsecured.
Olvera was arrested on charges of child endangerment, and the guns were seized.
Officers also found a BB gun resembling a real gun in the teen's bedroom.
The 16-year-old was booked into juvenile hall on charges related to criminal threats and firearm offenses.