Bomb squads did not find any explosives on an initial sweep but are continuing to search the large campus.
Officials didn't immediately know what connection there might be between the medic and San Clemente High School. One of the gates to the sprawling military base is just a couple of miles from the school.
A search was launched for the missing medic, but officials do not believe any military-grade explosive was stolen from the base, said Marine Lt. Joshua Benson.
"Nothing has been stolen from Camp Pendleton. Right now all we know is there was threatening information on a piece of paper," Benson said.
The medic was identified as Daniel Morgan, 22.
He is white, wears glasses, has short hair and is driving a white Jeep Wrangler with a black top, with license number 6NKZ930, said Orange County Sheriff's Department spokesman Jim Amormino.
About 3,200 students and 180 faculty members were taken to the Tritons football field shortly after the school was alerted at 8:45 a.m. Wednesday. Bomb squads and bomb-sniffing dogs from the military and several law enforcement agencies swept the field before opening it to students.
The search moved inside. As the gymnasium, auditorium and other rooms were cleared, the students were taken into the air-conditioned rooms.
Morgan was last seen at the base at 5 p.m. Tuesday, Amormino said. When he failed to show up for work Wednesday, his barracks were searched and the note was discovered, he explained.
The note claimed he had placed explosive devices in and around the school, Amormino said.
"The campus is secure," he said around noon. "We have every available bomb-sniffing dog in the county here searching room by room."
The FBI and county fire officials also were involved, he said.
"We're taking it very seriously ... it's a threat from a military person who's not at work," he added.
The school posted a message to parents, in English and Spanish, advising them not to go to the school. "Security personnel and officers are guarding the stadium and prohibiting entry onto the campus," the note said.
It also provided a rumor control hotline if parents wanted additional information.