The Faculty of science is as old as Egerton University as an institution of higher learning. Basic science courses namely chemistry, Physics, Botany, Zoology and mathematics were offered to diploma courses since the establishment of the Egerton college as an institution of higher learning in 1950s. In 1986, when Egerton college was elevated to a University college status and various programmes in agricultural science were introduced it was realized that there is need to describe courses to strengthen these programmes in basic science and more courses were introduced as pre-requisites.

This lead to the creation of the Faculty in 1987 when Egerton University was given a full University status. The primary role of the Faculty was to provide appropriate facilities for the advancement of basic scientific knowledge to students and scholars within the Faculty and to other Faculties. The first Bachelor of Science students majoring in Basic Sciences were admitted for the 1987/88 Academic Year. During this time there were two departments namely Biological Sciences and Physical Sciences. Science students pursued Bachelor of Science programme leading to specialization in Botany, Zoology, Physics, Chemistry, Mathematics, Statistics and Computer science under the 3.2.2. options. The Faculty also offered service courses to other Faculties mainly Education and Agriculture.

The first Bachelor of Education in Science students were admitted in 1988/89 Academic Year and they majored in teaching subjects offered by Faculty of science. Later six departments were created namely Botany, Zoology, Computer Science, Mathematics, Physics and Chemistry. The Faculty of science has continued to offer courses to all other faculties in areas of Botany, Zoology, Chemistry, statistics, computer science and physics majority being to Education and Agriculture.