Officers were forced to subdue the student with capsicum sprayed after allegedly threatening a classmate at the Garden Terrace school.
The 16-year-old Mile End boy was charged with carrying an offensive weapon and will front the Adelaide Youth Court on December 8.
Meanwhile, a primary school north of Gawler was thrust into lock down after a chemist was held up at gunpoint on Kingfisher Drive at Hewett around 3pm on Wednesday.
The brazen thief allegedly threatened staff with a gun before fleeing on foot with some cash, prompting the nearby primary school to go into lockdown.
Police are continuing their search for the man and urge anyone with information to contact Crime Stoppers on 1800 333 000.
For Australians looking for intelligent and unbiased news coverage, join renowned journalist Natarsha Belling on Your Morning Agenda for breaking national and international stories as well as the top business and finance stories - every weekday from 6:30am on Listnr