The De­part­ment was established on May 17, 1969, with the approval of the Min­is­try of Edu­ca­tion, and an Eve­ning Di­vi­sion was added in 1972. In 1985, the Grad­u­ate In­sti­tute of His­tory and Phi­lol­ogy was founded, comprising a Chi­nese Lit­er­a­ture Di­vi­sion and a His­tory Di­vi­sion. In 1993, the two divisions became separate institutes, and the His­tory Di­vi­sion was renamed the Grad­u­ate In­sti­tute of His­tory, admitting master's students. The PhD Pro­gram began admitting students in 1997. In response to changing social conditions, the Eve­ning Di­vi­sion was reorganized as the Di­vi­sion of Con­tin­u­ing Edu­ca­tion in 1997 and stopped admitting students in 2000. Be­gin­ning in 2003, the De­part­ment offered an In-service Master's Pro­gram with evening classes; having fulfilled its interim continuing-education mission, the program received approval to discontinue admissions in Ac­a­demic Year 2010–11. The De­part­ment currently offers undergraduate, master's, and PhD programs.

The De­part­ment is housed in NCKU's Former Lib­eral Arts Build­ing, a national monument in Tainan, Taiwan's historic capital. The building originally served as the Bar­racks of the Im­pe­rial Jap­a­nese Army's Taiwan 2nd In­fan­try Reg­i­ment. The De­part­ment is the only history department in Taiwan with a building of its own. In the 1970s, the De­part­ment collaborated with the Harvard-Yenching In­sti­tute on research in Taiwan history, becoming a pioneer in Taiwan history research among Taiwan's universities. Through the His­tor­i­cal Site Survey field program, in which teachers and students learn from one another, the De­part­ment has collected many Tai­wan­ese historical artifacts, some of which are now held in the Na­tional Cheng Kung Uni­ver­sity Mu­seum of His­tory. As a result, teaching and activities centered on the Mu­seum of His­tory have become another distinctive feature of the De­part­ment.

The De­part­ment has a strong faculty whose research and teaching cover a wide range of fields. Geo­graph­i­cally, they span Taiwan, China, North­east Asia, South­east Asia, and the Middle East, as well as Greece, Rome, Brit­ain, France, Ire­land, Ger­many, and more. Within Chi­nese history, expertise ranges across the pre-Qin, Wei–Jin, Song–Yuan, Ming–Qing, and Re­pub­li­can periods. In Taiwan history, the focus is on economic, commercial, art, literary, cultural, and colonial history. In terms of specialized and thematic approaches, the De­part­ment's work encompasses economic history, social history, religious history (Bud­dhism, Daoism, Chris­tian­ity, and Islam), intellectual history, art history, gender history, historiophoty (history in film and television), oral history, history education, historical theory, public history, ecological history, the history of human–animal relations, the history of West­ern science and technology, the history of medicine, the history of care, and smart humanities. In all of these areas, the De­part­ment offers a comprehensive curriculum and has produced a rich body of research.