PurposePharmacy chains can differ with respect to the characteristics of their patient populations as well as their nonprescription products, services, and practices, and thus may serve as a surrogate for potential unmeasured confounding in observational studies of prescription drugs. This study evaluates whether a single‐source drug can have different patient outcomes based on the dispensing pharmacy chain.MethodsSeparate analyses for two anticoagulant drugs, rivaroxaban and apixaban, were conducted using Medicare Fee‐for‐Service claims evaluating the association between dispensing pharmacy chain and outcomes of acute myocardial infarction, ischemic stroke, intracranial hemorrhage, gastrointestinal (GI) bleeding, all‐cause mortality, and major GI bleeding. Inverse probability of treatment weighting (IPTW) was used to balance baseline covariates across pharmacy chain cohorts, and outcome association was assessed with a Cox Proportional Hazards model.ResultsWe observed no differences in outcomes across pharmacy chains for apixaban recipients. Rivaroxaban recipients from pharmacy chain C, however, had lower rates of GI bleeding (adjusted HR 0.83; 95% CI 0.69–1.00) and ischemic stroke (adjusted HR 0.57; 95% CI 0.38–0.87) as compared to chain A in primary analyses with a 3‐day grace period. The results moved closer to the null when 14‐ and 30‐day grace periods were implemented.ConclusionsThese results suggest that dispensing pharmacy chains may have the potential to act as a confounder of associations between drug exposure and outcome in some observational studies. Additional studies of potential confounding by pharmacy chain are needed. Further evaluation of potential pharmacy chain effects on safe use would be of value.