After leaving CHS, Stuart read the Natural Sciences Tripos at Trinity College, Cambridge. He stayed on to complete a PhD with Malcolm Clark, before moving to Harvard to do post-doctoral research with F. H. Westheimer. Stuart returned to Trinity as a research fellow and subsequently took up a post as a teaching fellow at Churchill College in 1971. He remained a lecturer and researcher in the Department of Chemistry at Cambridge until his retirement in 2006.
He won the Royal Society of Chemistry Bader Award in 2002. His research group (the Warren Group) is renowned for having produced some of the most successful organic chemistry academics in the United Kingdom. Stuart is also well known for his numerous university-level chemistry textbooks. He is perhaps best known as one of the authors of the best-selling undergraduate text Organic Chemistry, which he wrote with his former students Jonathan Clayden and Nick Greeves, and fellow Cambridge lecturer Peter Wothers.