Students at Crescenta Valley High School were evacuated at around 2 p.m. to a nearby church after the man, who was carrying a duffel bag, reportedly tried to enter without being authorized.
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At 3:20 p.m., deputies with the Los Angeles County Sheriff's Department found the suspect at a Starbucks in the 3500 block of Foothill Boulevard in Glendale.
They said a school staff member, who had seen the suspect, came to the location and positively identified him.
Video obtained by Eyewitness News shows the moment the suspect was placed in handcuffs.
Deputies said the suspect wasn't carrying any weapons.
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The sheriff's department said investigators don't know why the suspect wanted to enter the school.
He has since been booked at Crescenta Valley Sheriff's Station. The incident remains under investigation.