Pioneer Junior College was established on 2 January 2000, under the leadership of the first Principal, Mr Kwek Hiok Chuang. The College functioned at the holding site, 10/12 Science Centre Road from Jan 2000 to Dec 2002. 62 teachers and executive and administrative staff, together with 750 students were the pioneer Pioneers. Students were involved in the formation of college rules and design of college crest and uniform. It was the first college to allow two sets of uniform designs for both boys and girls. It was also the first college to allow girls to wear dress pants as part of the uniform. The College vision and mission statements were formally endorsed by the stakeholders, ie the College Advisory Committee, the parents, the staff and students on 31 Aug 2000. In the subsequent year, the college anthem and flag were formally adopted by the college community on 8 Aug 2001. The colour of the college uniform was changed from the blue top to the present white top in Dec 2001.

We are the first college to launch our own Satellite Ground Receiving Station on 25 Feb 2002. The Inaugural College Day was held on 26 Apr 2002 to award deserving pioneers who have contributed in one way or another to the college. The Guest-of-Honour was the Chairman of the College Advisory Committee, Prof Phua Kok Khoo.

The College was relocated to its present location, 21 Teck Whye Walk on 19 Dec 2002.

The College was officially opened by Mr Tharman Shanmugaratnam, Acting Minister of Education, on 20 Feb 2004.

In Dec 2005, Mrs Tan-Kek Lee Yong became the College’s second principal.