Kyoto Imperial University was founded in June 1897 and the College of Science and Engineering was established in September of the same year as the first of several colleges in a confederation of colleges comprising the university.

In July 1914, the College of Science and Engineering was split into the College of Science and the College of Engineering.

In February 1919, the system of a confederation of colleges evolved into a system of faculties, and the College of Engineering became the Faculty of Engineering.

Since its establishment, the Faculty of Engineering has constantly sought to expand and develop in response to the academic and social demands of the times while sharing the same historical timeline as the university. It stands today as the university's largest faculty and is engaged in activities and initiatives that deal with almost all fields of engineering.

A program of restructuring undertaken by the Faculty of Engineering to reflect the emphasis on graduate school resulted in the establishment of the School of Industrial Chemistry in 1993, the School of Engineering Sciences in 1994, the School of Electrical and Electronic Engineering and the School of Informatics and Mathematical Science in 1995, and the School of Global Engineering and the School of Architecture in 1996, and heralded the launch of a new Faculty of Engineering for the twenty-first century.

The Graduate School of Engineering was established in 1953.

With the implementation of the four-year plan to emphasize graduate school education from 1993 to 1996, 157 courses (small courses) belonging to each department of the Faculty of Engineering were reorganized into 25 departments of the Graduate School of Engineering. Also, the emphasis on the graduate school has led to the establishment of a number of new departments and started to conduct graduate education and research appropriate for the new era.

In addition, the emphasis on graduate school has encouraged the reorganization of existing graduate schools and the creation of new graduate schools, including some departments that used to be part of the Graduate School of Engineering. Eventually, there are now 17 departments in the Graduate School of Engineering.