Two male students are being investigated on suspicion of planning "an assault on students and staff" at San Ysidro High, according to San Diego police.
The school has had eight telephone bomb threats in recent weeks but, so far, no evidence links the two students to those "terrorist" calls, police said.
The students have not been charged, but an investigation continues.
"We take these threats very seriously and investigate each incident to the fullest," said Lt. Terence Charlot.
The police department is working with the Sweetwater Union High School District, the juvenile division of the district attorney's office and a multiagency task force concerned with Internet crimes against children.
Bomb threats have also been made in recent weeks against schools in La Jolla and Carlsbad. No arrests have been made.