Universitas Negeri Manado (Unima) was established in 1955 under the name Perguruan Tinggi Pendidikan Guru (PTPG) Tondano, based on the Decree of the Minister of Education, Teaching, and Culture of the Republic of Indonesia No. 24511/Kab/1955 dated September 22, 1955. At that time, there were 17 departments, including four science departments: Mathematics, Natural Sciences, Chemistry, and Biology. In 1956, PTPG Tondano became the Faculty of Teacher Training and Education (FKIP), which was incorporated into Universitas Hasanuddin (UNHAS) and based in Tondano. In 1958, FKIP UNHAS was relocated to Manado. The science departments still active at that time were Biology and Mathematics.

The institution continued its development:

• In 1961, it became FKIP SULUTENG in Manado.
• In 1963, it became the Manado branch of IKIP Yogyakarta.
• In 1965, it was designated as IKIP Negeri Manado, operating independently with five faculties, one of which was the Faculty of Teacher Training in the Exact Sciences (FKIE).

FKIE continued to grow, undergoing multiple leadership transitions. In 1982–1983, based on Presidential Decree No. 71 of 1982 and the Decree of the Minister of Education and Culture No. 0157/O/1983, FKIE was transformed into the Faculty of Mathematics and Natural Sciences Education (FPMIPA). FPMIPA continued to develop, with several changes of deans and vice deans over various periods:

• In 1992, the IKIP Negeri Manado campus was moved to Tonsaru (Tondano), Minahasa Regency.
• From 1996 to 2000, FPMIPA was led by Dr. M.J. Rampengan, M.Pd.
• In 2000, IKIP Negeri Manado officially became Universitas Negeri Manado (Unima) through Presidential Decree No. 127 of 2000, and FPMIPA was renamed FMIPA.

FMIPA continued expanding with various structural leadership changes, the addition of the position of Fourth Vice Dean, and the strengthening of academic programs. In 2022, based on the Regulation of the Minister of Education, Culture, Research, and Technology of the Republic of Indonesia No. 17 of 2022 concerning the Organization and Working Procedures of Unima, the faculty’s name was changed to the Faculty of Mathematics, Natural Sciences, and Earth Sciences (FMIPAK). The term Vice Dean Assistant was also replaced with Vice Dean.

As of 2025, FMIPAK is led by:

• Dean: Prof. Dr. Mokosuli Yermia Semuel, M.Si.

• Vice Dean for Academic Affairs: Mercy M. F. Rampengan, S.Pi, M.App.Sc, Ph.D.

• Vice Dean for Finance and General Affairs: Dr. Nicky Kurnia Tumalun, M.Sc

• Vice Dean for Student Affairs and Alumni: Dr. Nova L. I. M. Ogi, M.Si.

Currently, FMIPAK of Universitas Negeri Manado oversees five departments: Mathematics, Biology, Physics, Chemistry, and Science Education.