[3] The large enrolment numbers and other factors led to the introduction of the "sub-school" system at Hamilton Senior High School from 1975, consisting of three lower-school sub-schools—Delta, Grinceri (later renamed Leda), and Omega—each containing students from years 8 to 10, with students in years 11 and 12 in a separate upper school.

On 12 December 1962 a worker, Velko Garbin, suffered fatal injuries sustained by a nail gun incident during the construction of the school.

The school suffered an arson attack in 2010 when a metal shed was set alight, causing A$100,000 in damage.

From 2018, Hamilton Senior High School students joined students of the also-defunct South Fremantle Senior High School to form Fremantle College.

The buildings of the former Hamilton Senior High School were earmarked for demolition and the land designated for housing.