After obtaining his Ph.D., Stevens accepted a postdoctoral position in 1988 in the lab of Nobel Laureate William N. Lipscomb, Jr. in the chemistry department at Harvard University where he focused on the large allosteric enzyme aspartate carbamoyltransferase.
In 1991, he accepted a tenure-track position at the University of California, Berkeley in the chemistry department with a joint appointment in neurobiology. His initial research as an assistant professor focused on structural neurobiology and immunology, combining chemistry, structural biology and protein chemistry with a specific biological interest in understanding how the G protein-coupled receptor (GPCR) superfamily works. A seminal collaboration for Stevens was with Professor Peter G. Schultz where they jointly published a series of Science and Nature papers describing the immunological evolution of antibodies through careful structural studies. In 1999, Stevens left Berkeley to take a tenured position at The Scripps Research Institute. While at The Scripps Research Institute, Stevens has helped to found and establish the Joint Center for Structural Genomics, Joint Center for Innovative Membrane Protein Technologies, and the GPCR Network, all funded by the National Institutes of Health with direct guidance from NIGMS.  In 2012, Stevens co-founded the  at ShanghaiTech University. In 2014, Stevens moved his lab from The Scripps Research Institute to the University of Southern California, where he is currently the Provost Professor of Biological Sciences and Chemistry and he founded the Bridge Institute to converge the arts and sciences.
Stevens is known for obtaining the structures of many biologically significant proteins and his technological innovations. He is considered a pioneer of high-throughput x-ray crystallography and structural genomics. His laboratory has led to the contribution of over 500 protein structure entries in the Protein Data Bank www.pdb.org. Stevens has withdrawn two different structures of ligand-bound clostridial neurotoxins.
In October 2007, Stevens and colleagues published the first high-resolution structure of a human GPCR.  The β-adrenergic receptor work was quickly followed up 9 months later by the determination of the structure of the human A adenosine receptor structure, also known as the caffeine receptor. In 2010, the structures of the human chemokine CXCR4 receptor (HIV co-receptor), the human dopamine D3 receptor and the human Histamine H1 receptor were published. In addition to these inactive-state structures, Stevens and colleagues solved the structure of an agonist-bound A adenosine receptor.
Subsequent novel human receptor structures include:
2012: The first structure of a lipid-activated GPCR, the sphingolipid, the human kappa-opioid receptor and the human nociceptin/orphanin FQ peptide receptor.
2013: Serotonin receptors 5-HT1B and 5-HT2B, the second HIV co-receptor, C-C chemokine receptor type 5 (CCR5)  and the first structure of a non-class A GPCR, the transmembrane domain of the human Metabotropic glutamate receptor 1 (mGluR1)  and the first structures of non-rhodopsin family GPCRs, the transmembrane domain of the human Smoothened receptor from the Frizzled/Taste2 family  and the transmembrane domain of the human glucagon receptor (GCGR) from the adhesion (class B) family.
2014: The human P2Y receptor 12 (P2Y12) bound to antagonist or agonist;  the human Delta opioid receptor at 1.8A  and the first structure of a class C GPCR, the transmembrane domain of the human Metabotropic glutamate receptor 1 (mGluR1).
2015: The human Lysophosphatidic acid receptor 1 (LPAR1), the human angiotensin II receptor type 1 (AT1R),  human P2Y receptor 1 (P2Y1); and the human Rhodopsin-Arrestin complex.
2016: The marijuana receptor—human Cannabinoid receptor type 1 (CB1)  and the human C-C chemokine receptor type 2 (CCR2) 
2017:The human apelin receptor  and the human angiotensin II receptor 2 (AT2R)  as well as the full length human glucagon receptor (GPCR) and trans membrane domain of the human glucagon like peptide receptor 1 (GLP1R) 
2018: The human seratonin receptor 5HT2C   human neuropeptide Y Y1 receptor   platelet activating factor receptor   and the trans membrane domain of the human frizzled 4 receptor 
2019: The human prostaglandin E2 receptor3 (EP3), the human cannabinoid receptor CB2, the human neurokinin 1 receptor, and the melatonin receptors MT1  and MT2 
2020:The human melanocortin 4 receptor (MC4),
In combination with the structural studies, working with the computational biology community to conduct GPCR Dock 2008 and GPCR Dock 2010 has helped to evaluate where the field is at, and functional studies using HDX and NMR are conducted by Stevens and collaborators to understand how the receptors work at the molecular level, and what fundamental and basic insights can be gained towards developing therapeutic drugs.