Birgit Kellner studied Tibetan and Buddhist Studies, Japanology, Philosophy and Linguistics at the University of Vienna (1987–1994) and completed her PhD in Indian Philosophy at the University of Hiroshima in 1999.

She conducted several post-doctoral research projects funded by the Austrian Science Fund FWF at the University of Vienna from 1999 to 2009, received a fellowship from the Alexander von Humboldt Foundation to conduct research at the University of Hamburg from 2002 to 2003, and was a Visiting Assistant Professor at the University of California, Berkeley, in 2008. She was appointed Assistant Professor at the University of Vienna in 2009.

Soon thereafter, she was appointed Professor for Buddhist Studies and Principal Investigator at the Cluster of Excellence "Asia and Europe in the Global Context" of the University of Heidelberg (W-3) (2010–15). Since 2015 she has served as Director of the IKGA at the Austrian Academy of Sciences. She also has served as Principal Investigator in the FWF special research area "Visions of Community – Comparative Approaches to Ethnicity, Region and Empire in Christianity, Islam and Buddhism (400–1600 CE)" from 2016 to 2019, and is currently directing the FWF project "Rationality, Meditation and Liberation in Indian Buddhism" (2019–23).

Birgit Kellner is Full Member of the Austrian Academy of Sciences (since 2021), Adjunct Professor at the University of Heidelberg, Fellow of the Alexander von Humboldt Foundation, Vice President of the International Association of Buddhist Studies, and Member of the Board of Directors, Buddhist Digital Resource Center (BDRC).