Administrators say a student resource officer spotted the student at the Centennial High gym. No students were supposed to be there at the time.
When the resource officer confronted the student, he ran off. Centennial, Lowell Scott and nearby Joplin Elementary were in lockdown for about an hour while police made sure students were safe.
The student in question still has not been found.
The district is on high alert after text messages started going around earlier in the week that a gunman would target Centennial on Friday.
Officials say extra police patrols will be around the schools Friday.
Threats have also spread into Canyon County.
The Vallivue School District said Thursday that it's aware that the threat rumors have spread to the Caldwell area. Officials at the district are working with Caldwell Police, but so far no specific or credible threats have been found.
Caldwell Police will have extra patrols at both the Caldwell and Valliuve schools Friday.
Nampa Police say they are also planning on additional patrols around schools to be extra cautious.
The Boise School District does not have classes on Friday.
The Coeur d'Alene School District has canceled classes Friday due to threat rumors.
The Post Falls School District has also closed its schools on Friday.
The district said in a statement: "Although we are reluctant to cancel school because the rumors are unsubstantiated, we feel it is the most appropriate decision based on the overall concern and angst as a result of the school violence related to last week's tragic events in Connecticut. The ability for students to have a calm learning day in the district has been compromised by the anxiety that the rumors have created."
The Lakeland School District in Rathdrum has also canceled classes.