The brothers also are charged with felony burglary and misdemeanor vandalism in connection with the blaze, which happened at a portable classroom used for art class and storing art supplies at the school, which is located at 470 El Paseo Drive.
Deputy District Attorney Scott Swisher said the misdemeanor vandalism charges could be upgraded to felony charges if authorities can prove the fire caused more than $400 in damage.
Fire officials have estimated that the blaze caused more than $40,000 in damage.
According to Oakland police, the two brothers live near the school and used to go to school there.
The older brother now attends Fremont High School in Oakland and the younger brother attends Madison Middle School.
The burglary charges stem from allegations that the brothers stole some colored marker pens from the school.
Swisher said the brothers are being held at Alameda County Juvenile Hall in San Leandro.