Stephan Sanders trained as a pediatric physician in the United Kingdom before pursuing a career in genomics and bioinformatics research as a graduate student and postdoctoral researcher in the laboratory of Matthew State at Yale University. In 2014, he moved to the University of California, San Francisco to start his own lab in the Department of Psychiatry.

His research has helped characterize the role of rare and de novo genetic variants in the etiology of neurodevelopmental disorders, including identifying many genes that contribute to autism risk. He has used these gene lists to provide insights into the cell types and biological processes that underlie autism and to investigate genotype-phenotype relationships, including autism sex bias and variants in the sodium channel gene SCN2A. Recently, Sanders has played a leading role in using whole-genome sequencing data to extend rare variant methods to noncoding variants in autism and other neurodevelopmental and psychiatric disorders.