In July 1961 a second Faculty of Science of the University of Ceylon was established at Peradeniya, to accommodate the enhanced intake of students into higher education in science. As in Colombo, the second faculty consisted of five Departments, namely Botany, Chemistry, Mathematics, Physics and Zoology, and the students were admitted into two streams-Biological Sciences and Physical Sciences. The first Batch of students at Peradeniya consisted of forty Biological Science students and seventy six Physical Science students. Though two Faculties of Science continued to exist both at Colombo and Peradeniya, the Dean of the Faculty of Science as well as the Heads of the Department were in Colombo. Lectures and practicals on identical syllabi were conducted and at the end of the year, the students appeared for the same examination. Those who scored high marks at the G.S.Q. Examination, opting to study Special Degree Courses in appropriate subjects, were transferred to Colombo.

A Department of Geology was created at Peradeniya in 1964 and a new General Degree subject combination of Chemistry, Geology and Physics was introduced. There were four subject combinations available in Physical Sciences while one subject combination was available in the Biological Science stream. Until 1996, the first year Engineering and Agriculture students followed the G.S.Q. Course in the Faculty of Science.

In 1967, National Council of Higher Education was established and the two campuses were made into two independent Universities. The University at Peradeniya was named the University of Ceylon, Peradeniya. The Faculty of Science retained, more or less, the same syllabi, examination structure, etc. to which it was accustomed, and in addition, Special Degree Courses were started. In 1971,the Faculty commenced conducting Science Courses in the Sinhala and Tamil media in addition to the English medium, thus helping those students who entered the Faculty in the swabasha medium.

With the establishment of a single University under the University of Sri Lanka Act No.1 of 1972, University of Ceylon, Peradeniya became one of the five campuses of the University of Sri Lanka. The Vice Chancellor was Professor B.A.Abeywickrama who was on leave from the Department of Botany of this Faculty. Dr.S.U.Kodikara became the President of the Peradeniya Campus and Professor V.Appapillai becomes the Dean of the Faculty of Science.

By the Universities Act NO.16 of 1978, the campuses regained the autonomous university status and, the Peradeniya Campus thus becomes the University of Peradeniya.Also it become the legatee of the former University of Ceylon. The first Vice-Chancellor of the University of Peradeniya was Professor B.L.Panditharatna and Professor H.W.Dias was elected the Dean of the Faculty of Science. The Faculty admitted 55 Biological Science Students and 128 Physical Science Students for the first year courses, and the total student population in the Faculty was 608. Among the academic staff were six professors, six associate professors and ten senior Lecturers. The Faculty Continued to conduct the Degree Courses in Sinhala, Tamil and English media. In 1981 the examination structure of General and Special Degrees was changed. The new structure introduced separate Part 1 and Part 2 examinations for the General Degree and additionally a Part 3 examination for Special Degrees. In 1984, a Computer Unit was established in the Faculty. An English Language Teaching Unit (ELTU) was established in 1986 to assist Sinhala and Tamil media students. Both these units were established with the initiative of the University Grants Commission.

In 1998, Professor R.P.Gunawardane became the Dean of the Faculty and held this post till February 1991. A Science Education Unit (SEU) was set up in the Faculty in January 1989, with the main aim of popularizing Science among the public and especially among the school children. Computer Science was introduced as a subject in 1990 and the number of subject combinations available in the Physical Science stream was increased to 7. Prof H.H.G.Seneviratne was elected the Dean in 1991. As a part of the golden jubilee celebrations of the University, a Jubilee Science Exhibition was held in 1992.

In 1994, Prof R.P.Gunawardane was again elected the Dean of the Faculty. In 1995, the Structure and Curricula of Undergraduate Courses underwent significant and far-reaching changes. These Changes have brought about the flexibility and broad basing of the Science Degree Programs. The Scheme of evaluation has also undergone a revision. The Course Contents of all the Courses have been revised and updated. Two new departments – the Department of Molecular Biology & Biotechnology and the Department of Statistics and Computer Science was commenced in 1997. Computing and Communication facilities in the Faculty have been expanded considerably. A Postgraduate Institute of Science (PGIS) was established in 1996 at the premises of the Faculty of Science on a proposal made by the Faculty Board of Science. The Postgraduate Institute of Science is a National institution established for the purpose of promoting, organizing and conducting postgraduate programs and research in science.