Warfarin is a widely used anticoagulant, and its S‐enantiomer has higher potency compared to the R‐enantiomer. S‐warfarin is mainly metabolized by cytochrome P450 (CYP) 2C9, and its pharmacological target is vitamin K epoxide reductase complex subunit 1 (VKORC1). Both CYP2C9 and VKORC1 have genetic polymorphisms, leading to large variations in the pharmacokinetics (PKs) and pharmacodynamics (PDs) of warfarin in the population. This makes dosage management of warfarin difficult, especially in the case of drug–drug interactions (DDIs). This study provides a whole‐body physiologically‐based pharmacokinetic/PD (PBPK/PD) model of S‐warfarin for predicting the effects of drug–drug−gene interactions on S‐warfarin PKs and PDs. The PBPK/PD model of S‐warfarin was developed in PK‐Sim and MoBi. Drug‐dependent parameters were obtained from the literature or optimized. Of the 34 S‐warfarin plasma concentration‐time profiles used, 96% predicted plasma concentrations within twofold range compared to observed data. For S‐warfarin plasma concentration‐time profiles with CYP2C9 genotype, 364 of 386 predicted plasma concentration values (~94%) fell within the twofold of the observed values. This model was tested in DDI predictions with fluconazole as CYP2C9 perpetrators, with all predicted DDI area under the plasma concentration‐time curve to the last measurable timepoint (AUClast) ratio within twofold of the observed values. The anticoagulant effect of S‐warfarin was described using an indirect response model, with all predicted international normalized ratio (INR) within twofold of the observed values. This model also incorporates a dose‐adjustment method that can be used for dose adjustment and predict INR when warfarin is used in combination with CYP2C9 perpetrators.