The threat resulted in an immediate lockdown at the school, where all exterior and classroom doors were locked and students remained in the classroom with their teachers, according to a news release from the police service.
As a precaution, lockdowns were also instituted at the T.R. Leger alternative campus in Gananoque.
St. Joseph Catholic School and Linklater Public School were also put on alert.
Police said they located at a residence in Gananoque an unidentified suspect soon after the threat was made.
The young person was charged with two counts of uttering a threat to cause death, possession of a dangerous weapon, carrying a concealed weapon and possession of marijuana.
He was held in custody pending a bail hearing.
The lockdown and alert were removed from all schools at 12:20 p.m.