She holds a MPhil and a PhD in Economics from the University of Cambridge, held academic positions at University of Cambridge, University College London, University of Reading, and London School of Economics. She has published 15 books, more than 600 scientific papers, including publications in Nature, the Lancet, and top ranked economics, econometrics and sustainability science journals. She co-edited several prestigious academic journals, including Nature: Climate Action and Environmental and Resources Economics. She organized numerous international scientific conferences, supervised more than 30 PhD students, and gave keynote speeches and public lectures across the world.

Professor Koundouri is an academician, elected member of Academia Europae, European Academy of Sciences and Arts, World Academy of Art and Science (WAAS) , InterAcademy Partnership (IAP) , and member of the Nominating Committee for the Nobel Prize in Economics Sciences.

In 2019, she was elected President of the European Association of Environmental and Resource Economists (EAERE) the biggest scientific association in the field, with more than 1500 member institutions, from more than 75 countries and she is now chairing the World Council of Environmental and Natural Resource Economists Associations (WCERE). In 2022 she received the prestigious European Research Council Synergy Grant, and in 2023, she was awarded the Academy of Athens Award for Scientific Excellence.