The foundations of the Department of Bioengineering were laid in 2005, with the opening of the Bioengineering Master's Program under the Department of Chemical Engineering subjected to The Institute of Pure and Applied Sciences of Marmara University.

Bioengineering Department was founded by Prof. Dr. Ahmet Alp SAYAR, who was the Dean of Engineering Faculty between the years 2000 and 2009. He was also the founder of the Department of Chemical Engineering. Following the establishment of the Bioengineering Department, the Master's Program was transferred to the Bioengineering Graduate Program and in the 2008-2009 academic year, the Ph.D. program of the Department was accepted by YÖK and our Department started to accept students.

The Department of Bioengineering started to accept students to the undergraduate program in the 2010-2011 academic year. Department aims to provide its students with basic bioengineering and bioprocess engineering knowledge and skills, as well as technical elective courses in many different fields of bioengineering, such as biopolymers, protein engineering, proteomics, systems biology, biomaterials, environment, and industrial biotechnology.