The threat was made on Oct. 19. It was one of several that forced Districts 203 and 204 to change their schedules.
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Both boys are from Naperville and were charged with felony disorderly conduct.
They are 15 and 16, Naperville police said.
RELATED: Naperville North High School put on lockdown, school day canceled due to bomb threat
"Threats of school violence, whether written, spoken or posted on social media, are unacceptable and will not be tolerated. Parents, please talk to your children about the seriousness and potential consequences of such statements because we will continue to take them seriously and take necessary action to ensure the safety of our schools," Naperville Police Chief Jason Arres said.
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Police would not provide any details about the threat that was made.
A New York teenager was charged last month with making a threat against Naperville North High School.