Direct oral anticoagulants, like apixaban and rivaroxaban, are important for the treatment and prophylaxis of venous thromboembolism and to reduce the risk of stroke and systemic embolism in patients with nonvalvular atrial fibrillation. Since apixaban and rivaroxaban are predominantly eliminated by CYP3A and P-glycoprotein (P-gp), concomitant use of combined P-gp and strong CYP3A4 inhibitors and inducers should be avoided. Physiologically-based pharmacokinetic (PBPK) models for apixaban and rivaroxaban were developed to estimate the net effect of CYP3A induction, P-gp inhibition and P-gp induction by rifampicin. The disposition of rivaroxaban is more complex compared to apixaban since both hepatic and renal P-gp is considered to contribute to rivaroxaban elimination. Furthermore, organic anion transporter-3 (OAT3), a renal uptake transporter, may also contribute the elimination of rivaroxaban from systemic circulation. The models were verified with observed clinical drug-drug interactions with CYP3A and P-gp inhibitors. With the developed models, the predicted AUC and C max ratios were 0.43 and 0.48, respectively, for apixaban, and 0.50 to 0.52 and 0.72 to 0.73, respectively, for rivaroxaban when co-administered with 600 mg multiple dose of rifampicin and which were very close to observed data. The impact of each of the elimination pathways was assessed for rivaroxaban and inhibition of CYP3A led to a larger impact over intestinal and hepatic P-gp. Inhibition of renal OAT3 or P-gp led to an overall modest interaction. The developed apixaban and rivaroxaban models can be further applied to the investigation of interaction with other P-gp and/or CYP3A4 inhibitors and inducers.