School officials said the incident happened two weeks ago and involved a second grader. Police are still investigating the case.
"The school is safe as any other we have because of this incident we have taken measures to make sure are children are safe," said Manuel Paul, superintendent for the San Ysidro Unified School District.
Officials at Beyer Elementary said many volunteers have come forward to help monitor the campus and additional safety measures include putting up security cameras and making sure kids travel in groups when they leave the classroom.
"In any case involving young victims, information gathering is extremely sensitive and difficult," Munoz said. "At the point at which we make an arrest, we will notify the school administrators immediately."