Self‐controlled designs, specifically the case‐crossover (CCO) and the self‐controlled case series (SCCS), are increasingly utilized to generate real‐world evidence (RWE) on drug‐drug interactions (DDIs). Although these designs share the advantages and limitations of within‐individual comparison, they also have design‐specific assumptions. It is not known to what extent the differences in assumptions lead to different results in RWE DDI analyses. Using a nationwide US commercial healthcare insurance database (2006–2016), we compared the CCO and SCCS designs, as they are implemented in DDI studies, within five DDI‐outcome examples: (1) simvastatin + clarithromycin and muscle‐related toxicity; (2) atorvastatin + valsartan, and muscle‐related toxicity; and (3–5) dabigatran + P‐glycoprotein inhibitor (clarithromycin, amiodarone, and verapamil) and bleeding. Analyses were conducted within person‐time exposed to the object drug (statins and dabigatran) and adjusted for bias associated with the inhibiting drugs via control groups of individuals unexposed to the object drug. The designs yielded similar estimates in most examples, with SCCS displaying better statistical efficiency. With both designs, results varied across sensitivity analyses, particularly in CCO analyses with small number of exposed individuals. Analyses in controls revealed substantial bias that may be differential across DDI‐exposed and control individuals. Thus, both designs showed no association between amiodarone or verapamil and bleeding in dabigatran‐exposed but revealed strong positive associations in controls. Overall, bias adjustment via a control group had a larger impact on results than the choice of a design, highlighting the importance and challenges of appropriate control group selection for adequate bias control in self‐controlled analyses of DDIs.