From 2001 to 2004, he was Junior Research Fellow at Christ Church (a college of the University of Oxford) and a Research Fellow of the Welcome Trust at the Center for Mathematical Biology in the University of Oxford.  He was Assistant Professor of Informatics and Associate Director of the Biocomplexity Institute at Indiana University, Bloomington between 2004 and 2008.  In 2008, he joined the University of Michigan as Associate Professor of Molecular & Integrative Physiology and a U-M Brehm Investigator in the Brehm Center for Diabetes Research. In 2013, he was jointly appointed as associate professor in the Department of Computational Medicine and Bioinformatics.  He was promoted to professor in both departments in 2015, appointed as the John A. Jacquez Collegiate Professor of Physiology in 2016, and served as chair of the Department of Molecular & Integrative Physiology between 2017 and 2021. In 2021, he was appointed the William K. Warren Foundation Dean of the College of Science at the University of Notre Dame.
Schnell is Past-President of the Society for Mathematical Biology.  He served as the Editor-in-Chief of Mathematical Biosciences, and is a member of the Standards for Reporting Enzymology Data Commission.