Shuqun Primary School started in 1925 and was known as Tuan Cheng Public School. Later it became known as Seh Chuan High School. It was situated off Jalan Jurong Kechil.

In April 1983, Seh Chuan High School changed from an aided to a government school bearing the hanyu pinyin name of Shuqun Secondary School. In April 1984, the primary section ceased to function as part of the secondary school and became known as Shuqun Primary School.

In June 1986, headed by Mr Tear Ee Soon, Shuqun Primary School shifted to its present site with an enrolment of 533 pupils and 17 teachers.

From 15 December 1993, Mdm Wong Chwee Neo took over the running of the school. Miss Chan Wai Lin then became Principal from 1 January 2000 to 31 December 2003 followed by Mr Gary Tsu Chin Sun from 1 January 2004 to 14 December 2010 and Ms Geetha Doraisamy from 15 December 2010 to 15 December 2018. The current Principal is Mrs Sara de Souza who is accompanied by Vice-Principals Mrs Adeline Kee (Curriculum) and Mr Muhammad Fadylla Rashiman (Curriculum). Over the years, the pupil enrolment has increased to the current estimated 1462 and the staff to a strength of 124.