Police carried out a search following the report of a device being left in the area and have declared the report a hoax.
The Campsie Road has since been re-opened.
Inspector Keith Hicks said: “Huge disruption has been caused to pupils, staff, parents and members of the public here today.
“Police take all precautions to ensure the safety of the public.
“I would like to thank anyone affected by the alert today for their patience whilst officers searched the scene.
“I would also ask anyone with any information about those responsible for this incident to contact police in Omagh on 101.
“Information can also be passed anonymously to the independent charity Crimestoppers on 0800 555 111.”