From 2001 to 2010 Wallner worked at University of Vienna: starting as a pre-doc with a research project at the Institute for Ethics and Law in Medicine, then as a post-doc at the Department of Legal Philosophy, Law of Religion and Culture at University of Vienna's Faculty of Law.
From 2008 to 2010 Wallner was awarded the APART grant by the Austrian Academy of Sciences and persued his habilitation project at the Center for Clinical Bioethics at Georgetown University in Washington, DC.
In October 2010, he was appointed head of human resources and organizational development at Barmherzige Brüder Wien, in 2016 to his present position at Barmherzige Brüder Österreich. He has remained part of University of Vienna's Faculty of Law as Privatdozent.
Since March 2014, Wallner has been a member of the Austrian Bioethics Commission at the Federal Chancellery.