Costas Fotakis got his B.S. in Chemistry from National and Kapodistrian University of Athens in 1973 and his Ph.D. in Chemical Physics from University of Edinburgh in 1978.

From 1977-1983, he was Research Associate and Instructor at the University of Edinburgh and the Central Laser Facility of the Rutherford-Appleton Laboratory at Oxford University. In 1984, he joined the Univeristy of Crete as an Associate Professor, and, in 1989, he became Full Professor. He was the Chairman of the Scientific Board of the National Research Center 'Democritos' from 1994 to 1996 and the Director of the Institute of Electronic Structure and Laser (IESL/FORTH) from 1997 until 2013. From 2011 until 2016, he served as the Chairman of the Board of Directors of FORTH. From 2015-2019, he served as Alternate Minister responsible for Research and Innovation in the Ministry of Education. He retired and was elected Emeritus Professor at the University of Crete in 2017.

Fotakis was Springer Professor at the University of California, Berkley 2005-2006. He is a Fellow of OSA and a member of the Fellows Committee of the European Optical Society. He received an Honorary Doctorate from the Mediterranean University of Marseille.