Universitas Negeri Yogyakarta (UNY) was established as the Yogyakarta Teacher Training and Education Institute (IKIP) on May 21, 1964 with the issuance of the Decree of the Minister of Higher Education and Science. Based on the Decree of the Rector of IKIP Yogyakarta number 5 of 1965 regarding the organizational structure of IKIP Yogyakarta, one of the faculties at IKIP Yogyakarta is the Teaching Faculty of Exact Sciences (FKIE), which consists of the Department of Exact Sciences, Department of Natural Sciences, Department of Life Sciences, and Department of Chemistry.

In 1981, the Government Regulation (PP) of the Republic of Indonesia number 27/1981 was issued, concerning the arrangement of faculties at State Universities/Institutes. This regulation was followed by the Decree of the President of the Republic of Indonesia number 54 of 1982 concerning the Organizational Structure of the IKIP Yogyakarta, which stated that the name of FKIE was changed to the Faculty of Mathematics and Natural Sciences Education (FPMIPA). Likewise, the Department of Exact Science changed to the Department of Mathematics Education, with the stipulation by the Minister of Education and Culture of the Republic of Indonesia (SK no. 0554/0/1983) on December 8, 1983. At that time, the Department of Mathematics Education organized a Mathematics education study program. Considering that the minimum level of teacher education is Bachelor (S1), this department then only organizes the Bachelor of Education in Mathematics Study Program.

Simultaneously with the change of IKIP Yogyakarta into Yogyakarta State University (UNY), starting on May 29, 1997 the Department of Mathematics Education also organized a Bachelor of Science in Mathematics Study Program (SK Dirjen Dikti no. 1259/DT/T/97). There are five areas that are the focus of interest for students of the Mathematics Undergraduate Study Program, namely algebra, computers, analysis and geometry, applied mathematics, and statistics.

Given the high interest in Statistics and reviewing technological developments that increasingly require Statistics, in 2017 the Department of Mathematics Education opened the Bachelor of Statistics Study Program. This program was officially established with SK number 335/KPT/I/2017, and has accepted new students since the 2018/2019 academic year. In 2021, the Bachelor of Statistics Study Program will participate in BAN-PT accreditation and obtain good accreditation.