Denver police said the guns were found in a sweep of the school after the teenagers broke in into the building Monday night and ransacked several classrooms, NBC News reported.
Janitors had reported seeing two people inside the school about 10 p.m. Monday carrying what appeared to be rifles.
The Denver police department later tweeted that "what appeared to be assault rifles are more than likely BB guns."
Denver Police Chief Robert White said security video footage showed "one individual had made entry to the school and was waving the other individual into the school. The camera showed what appeared to be rifles."
The teens were arrested several hours after KIPP Montbello College Prep and Collegiate Prep Academy was surrounded by armored cars, a SWAT team and a bomb squad, KUSA-TV, Denver, reported.
The suspects are believed to have broken into Greenwood Elementary School about a mile from the academy about an hour earlier. Police responding to a burglar alarm at the elementary school said they found a broken window.
White alleged the teens, who are not believed to be students at the academy, intended to burglarize the school.
One of the janitors told police they saw two men in the school with rifles and backpacks, KUSA-TV said. Police officers said they saw one of the men carrying a large yellow pipe and were concerned the men may have had explosives.
Wisconsin business offering 'therapeutic cuddling' forced to close
Costly malfunction causes beer flood at Boston-area brewery