It was originally established at Fairfax (now Tokoiti) in the southeast of Milton, with Alexander Ayson as the first teacher.

As Milton grew in size due to the Otago gold rush in the early 1860s, a larger school was soon needed.

A new building was needed, as the Spenser Street site had been made to accommodate only some 200 children.

The new school, on the present site at the north end of Union Street, was opened in 1880.

The school's headmaster (its fourth) James Reid, was a keen student of chemistry, and technical subjects taught ranged from the "pure" sciences to agricultural studies and woodworking.