The history of the Biology Education Study Program at UIN Sunan Kalijaga Yogyakarta began with the long-standing development of the Faculty of Tarbiyah, which was first established in the 1960/1961 academic year as part of IAIN Sunan Kalijaga. The establishment of the faculty aimed to prepare educators and experts in the field of Islamic education. Over time, IAIN Sunan Kalijaga officially changed its status to an Islamic State University (Universitas Islam Negeri/UIN) based on Presidential Decree of the Republic of Indonesia Number 50 of 2004, which subsequently led to the renaming of the faculty as the Faculty of Education and Teacher Training (Fakultas Ilmu Tarbiyah dan Keguruan/FITK).

The specific development of the study program began in 1999, when it officially commenced operation under the initial name Tadris Biology Education within the faculty. The establishment of the program was aimed at producing educators and academics in biological sciences who are grounded in Islamic values. Following adjustments to academic nomenclature and governance, the study program was officially renamed the Undergraduate (S1) Biology Education Study Program in 2007.

Throughout its development, the quality of the curriculum and educational quality assurance within the Biology Education Study Program have undergone significant improvements. This achievement is demonstrated by the program's attainment of an “Excellent” accreditation status from the Indonesian Accreditation Agency for Education (Lembaga Akreditasi Mandiri Kependidikan/LAMDIK), based on Decree Number 626/SK/LAMDIK/Ak/S/VI/2023.

The strengthening of the learning process focuses on mastery of instructional design, learning process evaluation, and classroom management, supported by qualified teaching staff and modern biology laboratory facilities. In addition, the academic atmosphere of the study program has continued to develop through the integration of the Merdeka Belajar Kampus Merdeka (MBKM) program and the organization of scientific events such as the International Conference on Religion, Science and Education (ICRSE).

Currently, the Biology Education Study Program at UIN Sunan Kalijaga has established itself as an excellent educational institution that prepares graduates to pursue careers as educators, researchers, education managers, and edupreneurs. All aspects of the study program's development are directed toward integrating biological sciences based on local potential and technology, while consistently incorporating Islamic values to contribute to the advancement of civilization.