Ai Tong School started at a Methodist Church at Boon Tat Street in 1912 with about 30 pupils. In 1929, Singapore Hokkien Huay Kuan took over the school management. In 1955, when the construction of SHHK building was completed, Ai Tong moved into the building with Chong Hock Girls School (now named Chongfu Primary School).
In the seventies, urban renewal caused enrolment to drop and the School Management Committee decided to relocate the school to Ang Mo Kio. In 1990, Ai Tong School was among the pioneer batch of schools to be accorded SAP status. Plans were made to move the school to a larger site when enrolment soared. Ai Tong moved to 100 Bright Hill Drive on 9 July 1992.
The school has also attained many laudable achievements outside the classroom. In line with Singapore Hokkien Huay Kuan's objective to preserve Chinese language, values and culture, the school developed excellent programmes in essay writing, guzheng, wushu, Chinese dance, calligraphy, art and choir. Ai Tong also excels in basketball, volleyball and table tennis.