The Faculty of Mathematics and Natural Sciences is one of the faculties at UII which started accepting new students in 1995/1996 for the Department of Statistics, the Statistics study program. The opening of the Faculty of Mathematics and Natural Sciences is a demand and request from people who want to receive education in the field of science at the UII campus. Data from the Central Statistics Agency (BPS) shows that in Indonesia there is still a shortage of manpower from Science graduates (MIPA), which means that the number of requests for Mathematics and Natural Sciences graduates is greater than the graduates produced.

In the second year, based on the Decree of the Director General of Higher Education, Ministry of Education and Culture of the Republic of Indonesia No. 196 / DIKTI / Kep. / 1996 dated June 20, 1996, the Faculty of Mathematics and Natural Sciences obtained Registered status for the Department of Statistics, Statistics study program and Registered status for the Department of Chemistry, Chemistry study program. Thus, starting from the 1996/1997 academic year, the Department of Mathematics and Natural Sciences was the Department of Statistics plus one more department, the Department of Chemistry.

In order to enrich the department / study program, starting from the 1998/1999 academic year the Faculty of Mathematics and Natural Sciences opened a new department / study program, namely the Department of Pharmacy and starting in the 2002/2003 academic year the Pharmacist Professional Education program was opened. In the 2003/2004 academic year, the Faculty of Mathematics and Natural Sciences UII opened a D3 Chemical Analyst program which later changed its name to Diploma of Chemical Analysis Study Program. In 2014 the Chemistry Education Study Program was established and in 2018 the Chemistry Master Program was established. Three study programs in FMIPA currently have accreditation A, namely Chemistry, Pharmacy and the Professional Pharmacist. Meanwhile, the Statistics Study Program, Chemical Analysis and Chemistry Education are each accredited B.