The origin of Environmental and Biosystems Engineering at the University of Nairobi can be traced back to 1965 when the Department of Mechanical Engineering, Faculty of Engineering introduced a section in Agricultural Engineering focusing on Agricultural Process Engineering. The Department of Agricultural Engineering of University of Nairobi was established in 1975 originally as the Department of Agricultural Mechanization and Farm planning. The name was then changed in 1976 to Department of Agricultural Engineering.

In 2003, the University of Nairobi senate ratified the change of name of the Department and the degree program to Environmental and Biosystems engineering to reflect the content and intent of the Department's academic, research and consultancy services and to keep in tune with the expanding global challenges and demands.

As a University Department, the objectives of teaching, research, development and advancement of scientific knowledge in the application of engineering is captured through a dynamic curricular offered through undergraduate and post graduate programmes.