Authorities say the messages indicated that bombs were planted in the school.
The juvenile was arrested and released to his parents' custody after a hearing in the Kane County juvenile detention center.
If convicted, the student could receive probation or a more severe punishment.
"He could end up spending time in juvenile incarceration until he reaches age 21," said Chief James Lamkin of the St. Charles police.
"In addition to the criminal charges, the administration of the school district will be recommending an expulsion for the individual," said Supt. Donald Schlomann of School District 303.
The school superintendent said a $2,000 reward helped solve the case.