The University of Peradeniya is the legacy of the University of Ceylon first established in Sri Lanka in 1942. The Faculty of Science, comprising the Departments of Botany, Chemistry, Mathematics, Physics and Zoology were initially located in Colombo along with other Faculties of the University of Ceylon. It had been decided to have the permanent home of the University in Peradeniya and accordingly, the Faculty of Arts, Oriental Studies, Law, Agriculture, Veterinary and Dental Sciences were established at Peradeniya by the early part of the 1951-60 decade.

In 1961, the buildings of the Faculty of Science were made available at Peradeniya and the admission of the first batch of students took place in the 1961 –62 academic year. In order to accommodate the increasing demand for science education in the country the Faculty of Science in Colombo was allowed to form a second Faculty in Peradeniya and a part of the staff from the Colombo Faculty moved to Peradeniya Faculty at the early stages, while the latter gradually built up the staff by direct recruitment. Both branches of the Faculty functioned under common administration at each of the levels of department and faculty, with common curricula and examinations. In 1967 those segments of the University of Ceylon which were situated in Colombo were constituted as a separate and independent University. Thus, the second Faculty of Science at Peradeniya comes into being on its own, as the Faulty of Science, University of Ceylon, Peradeniya.