Drug‐drug interaction potentials of ensitrelvir, a novel oral inhibitor of 3C‐like protease of severe acute respiratory syndrome coronavirus 2, for drug transporters were evaluated by in vitro and clinical studies. The target drug transporters assessed were P‐glycoprotein (P‐gp), breast cancer resistance protein (BCRP), organic anion transporting polypeptide (OATP) 1B1, OATP1B3, organic anion transporter (OAT) 1, OAT3, organic cation transporter (OCT) 1, OCT2, and multidrug and toxin extrusion 1 and 2K. In vitro study revealed that ensitrelvir is a substrate for P‐gp and BCRP and inhibits P‐gp, BCRP, OATP1B1, OATP1B3, OCT1, and OAT3. Based on these results, a clinical drug‐drug interaction study to evaluate the effect of ensitrelvir on the pharmacokinetics of P‐gp, BCRP, OATP1B1, OATP1B3, and OCT1 substrates was conducted with a cocktail approach using digoxin (P‐gp substrate), rosuvastatin (BCRP, OATP1B1, and OATP1B3 substrate), and metformin (OCT1 substrate). The cocktail was administered first, and after the washout period, the cocktail was coadministered with 500 mg of ensitrelvir. No treatment‐emergent adverse events were observed. Pharmacokinetic analyses demonstrated that the ratios (90% confidence intervals) of “cocktail with ensitrelvir” to “cocktail without ensitrelvir” for maximum plasma concentration and area under the plasma concentration–time curve were, respectively, 2.17 (1.72‐2.73) and 1.31 (1.13‐1.52) for digoxin, 1.97 (1.73‐2.25) and 1.65 (1.47‐1.84) for rosuvastatin, and 1.03 (0.91‐1.16) and 1.02 (0.94‐1.11) for metformin. The results indicate that the exposure levels of digoxin and rosuvastatin increased when coadministered with ensitrelvir, but those of metformin were not changed. In conclusion, ensitrelvir has an impact on the exposure levels of P‐gp, BCRP, OATP1B1, and OATP1B3 substrates.