Abstract The debate on how neoclassical realism (NCR) has fared as a new brand of realism and supposedly a more rigorous approach towards foreign policy has become increasingly acerbic. Most NCR critics have challenged NCR’s epistemological positions, and few have scrutinised NCR’s methodological practice. This essay seeks to fill the void and focuses on the latter. My aim is both critical and constructive. Because NCR’s mainstay method is comparative case studies (CCSs), I first examine how NCR has practiced this method. I argue that NCR has been saddled with several key shortcomings when doing CCSs. Drawing from the extensive new qualitative methodology literature, I propose several remedies corresponding to the shortcomings. Fixing these shortcomings will allow NCR to advance more valid theories and move towards better theoretical synthesis. I then highlight qualitative comparative analysis as a very useful tool for NCR. Finally, I address a common criticism against NCR, that is, with numerous variables, NCR lacks theoretical synthesis and hence a theoretical core. I accordingly advance a preliminary framework for possible theoretical synthesis.