Founded in 1965, the school was the 61st one established by a newly independent Singapore, and one of two built that year. The school was an answer to requests made personally to PM Lee Kuan Yew by farmers when he visited the rural community of Yio Chu Kang. The original building was sited at the 11th milestone / 16 km Yio Chu Kang Road.
Officially opened by then Minister of Education Mr Ong Pang Boon, it started as an integrated English-Chinese stream school as part of government efforts to house two or more language streams under one administration and one principal. Thus, schools such as Yio Chu Kang Secondary School became a critical strategy in early nation building to emphasise the importance of bilingual education and to increase socialisation of students from different language mediums.