In 1960, under the vision and conviction of founding father, Rev Alan S Moore Anderson, the Presbyterian Synod passed the resolution to start a God-centred institution of learning and Li Sun High School was thus founded in 1965 at Upper Serangoon Road.
Before 2002, PHS occupied a small plot of land located across the road from the Yio Chu Kang MRT Station, and shared a field with the neighbouring Li Hua Primary School and Ang Mo Kio North Primary School, even though PHS shared no affiliations with either of these.