Professor Ynnerman is currently the head of the Media and Information Technology division at the Department of Science and Technology (ITN) at Linköping University and is the director of the Norrköping Visualization Center C. He is the head of a renowned research division in Visualization and Computer Graphics. He plays a leading role in the international visualization arena and is a frequently invited speaker at international conferences and other events.

During his career, Anders Ynnerman has held several key academic leadership positions. In 1996 he founded the National Graduate School in Scientific Computing (NGSSC) with funding from the Foundation for Strategic Research. He directed NGSSC until 1999. In 1998 Ynnerman was appointed the director of the National Supercomputer Centre (NSC), which is a focal point for high performance computing in Sweden. Under his leadership, NSC expanded rapidly and became the largest center for HPC in Sweden and took a lead as a technology transfer site in the area of cluster computing. NSC also deepened and expanded its collaboration with Saab AB and the Swedish Meteorological and Hydrological Institute (SMHI) during his time as director.

Ynnerman has chaired and hosted several international conferences including EuroVis 2007 and Eurographics 2010, the largest conferences in visualization and computer graphics in Europe. He served as the chair of the Eurographics association 2014–2016. He is currently the chair of the Eurographics working group on Data Visualization and the chairman of the EuroVis steering committee.