Yu was awarded a Royal Society University Research Fellowship in 2003, which allowed him to start his independent research towards the development of asymmetric C–H activation reactions. In 2004, he moved to Brandeis University as an assistant professor of chemistry. He moved to The Scripps Research Institute as an associate professor in 2007 and was promoted to full professor in 2010. In 2012, he was appointed the Frank and Bertha Hupp Professor of Chemistry.