After graduating from the Medical Faculty of University of Colombo, Sri Lanka, she started her career in 1982 as an intern medical officer. She became a university academic (in medical microbiology) in 1985, when she joined University of Ruhuna. She worked as a Research Fellow and an Honorary Senior Registrar in Virology at St George’s Hospital Medical School in London, UK form 1989–1993. She was promoted to the Professor in Microbiology in 2001 and currently holds the Chair in Microbiology of the Faculty of Medical Sciences of University of Sri Jayewardenepura- since 2001. She is a Fellow of the National Academy of Sciences of Sri Lanka.
She moved in to Science administration with her appointment as the Chairperson of the National Science Foundation of Sri Lanka in 2004. She continued in that capacity till 2013 and was reappointed to that post in June 2015. During the period of 2006 -2014 she was also appointed by the Cabinet as the Science Advisor to Minister of Science and Technology, the Senior Minister for Scientific Affairs and the Sector Specialist in Scientific Affairs.
Prof. Fernando in 2005 conceptualized and initiated the National Nanotechnology Initiative (NNI) and thereafter coordinated its implementation till 2010 with the establishment of Sri Lanka Institute of Nanotechnology (SLINTEC). In 2010 she also conceptualized and initiated the development of the National Science Technology and Innovation (STI) Strategy of Sri Lanka and thereafter played a leading role in the establishment of COSTI to coordinate the implementation of the National STI Strategy. Currently she is co-chairing the National Steering Committee to establish Sri lanka Biotechnology Institute (SLIBTEC) and the National Science Centre in Sri Lanka.
She is a member of the STI Advisory Board to the Executive Secretary of the UN Economic and Social Commission for Asia and the Pacific (UN-ESCAP).