As part of the Faculty of Engineering, the department was established in 1993. In 1993-1994, the program was started to train with 21 students in Mersin Metropolitan building. 1994-1995 academic year, Vocational School of Mersin University Çiftlikköy campus was moved to a portion of the building. Training was continued in classrooms and laboratories of Vocational High School in Mersin between 1994 and 1997. In the academic year of 1996-1997, the Faculty of Engineering Classroom Block was completed. Education continues in the 3 classrooms at the same building. Laboratory practices and research have been performed in the Laboratory Building since 2003. The department has 18 laboratories in the Laboratory Building. The department offers to undergraduate students a program of food processing, storage, transport, food production and the development of new knowledge and skills that can earn with the sciences of physic, chemistry and biology. The department has graduate programs leading to the Master of Science and PhD degrees. The department has offered the degree of Master of Science since 1993 and the degree of PhD since 2003. Undergraduate Program of Department of Food Engineering is reviewed during 2011-2012 evaluation period by Association for Evaluation and Accreditation of Engineering Programs (MÜDEK) and is accredited starting from May 1st, 2012 for five years.  MÜDEK also awarded EUR-ACE Label to undergraduate program of the department from May 1st, 2012 to September 30th, 2023. Undergraduate program of department has started compulsory English Preparatory Class since 2011-2012 academic year and 30% of the courses are tought in English.

The vision of Food Engineering Department is to be the leading research and education program at national and international area by offering undergraduate and graduate programs based on a continuous improvement approach by carrying out research projects with industrial partners and promotion of the exchange of academic staff and students with international institutes for the benefits of the society. The mission of Food Engineering Department is to establish undergraduate and graduate education program that is compatable to developing food technology and science; educate students to develop the self-assurance and analytical thinking ability that ables to solve the problems as an engineer, train the students to use and develop advanced technologies to produce safe and high quality foods; transfer research-based information and technology to the region, country and world; train the high qualified acdemics.