Master of Science Education Study Program Undiksha Postgraduate Program was established in 2009 with the Decree of the Director General of Higher Education No. 890/D/T/2009, dated June 11, 2009. Currently, the Master of Science Education Study Program is accredited B with accreditation certificate No. 3444/SK/BAN-PT/Akred/M/IX/2017.

Initially, the management of the Masters in Science Education Study Program was under the Undiksha Postgraduate Program until 2017. In line with the changes in Undiksha's OTK, the management of the master and doctoral programs in Undiksha was changed. Starting from the 2016/2017 academic year, the management of the Science Education Master's Degree Study Program is under the Undiksha Faculty of Mathematics and Natural Sciences (Undiksha Rector Regulation No. 105/UN.48/PP/2017). In 2020, at the discretion of the Undiksha Chancellor, the management of the Master of Science Education Study Program was again integrated into the Undiksha Postgraduate Program. Currently, the Master of Science Education Study Program is one of the master study programs under the management of the Undiksha Postgraduate Program.

The Master Program in Science Education Study Program aims to develop expert-level Science Education as a continuation of the development of the S1 Science Education Study Program. In accordance with the KKNI level (level 8), the Master of Science Education Study Program develops courses with a total weight of 40 credits which are translated into 14 courses including theses. These courses are offered in four semesters, with the focus on theoretical courses in the first two semesters and practical courses in the following two semesters. Practical lectures are focused on developing materials for the completion of the Thesis.

Graduates of the Master of Science Education Study Program are focused on having expertise in the fields of Science Education and Teaching and Science Education Research. As Science Education and Teaching Experts, graduates of the Master Program in Science Education Study Program are expected to be able to develop science education through research and professional practice as teachers. As an expert in the field of Science Education Research, graduates of the Master of Science Education Study Program are expected to be able to solve problems in the field of science learning through scientific research.