Fatta-Kassinos received a Diploma in Chemical Engineering from the National Technical University of Athens (NTUA), Greece, in 1993, and completed a M.Sc. in Environmental Management and Education in 1995 from the European Association of Environmental Management and Education (EAEME). She then received her Ph.D. in Chemical Engineering in 1999 from NTUA. Her dissertation was titled "Development of a methodology for the estimation of the pollution level of the groundwater aquifers in the vicinity of waste disposal sites." Following this, she served as a Postdoctoral researcher for three years at NTUA between 1999 and 2003.