The Department of Education (DOE) was established in July 1987, when the university was first upgraded to Taiwan Provincial Tainan Teachers College. Initially named the Department of Elementary Education (DOEE), it was dedicated to training professional elementary school teachers.

In 1991, the Graduate School of Elementary Education (GEEM)—now the master's and doctoral programs in Educational Entrepreneurship and Management (EEM)—was introduced. The master's program in Curriculum and Instruction (CIM) was launched in 2001.

In 2002, the Graduate Institute of Measurement and Statistics was established, offering a master's program in Measurement and Statistics (MSM). The department expanded further in 2003 by introducing a master's program in Technology Development and Communication (TDCM).

In 2004, following the university’s upgrade and renaming as the National University of Tainan (NUTN), the department was officially renamed the Department of Education (DOE). Further developments included the establishment of a doctoral program in Measurement and Statistics (MSD) in 2007 and a doctoral program in Curriculum and Instruction (CID) in 2009.

In 2011, the master's and doctoral programs in Educational Entrepreneurship and Management (EEM) and Measurement and Statistics (MS) were merged into the Department of Education.