In malignant biliary stricture (MBS), the diagnostic accuracy of ERCP‐based tissue sampling is insufficient. EUS‐guided fine needle aspiration biopsy (EUS‐FNAB) is emerging as a reliable diagnostic procedure. This study aimed to evaluate the usefulness of a diagnostic approach using ERCP‐guided transpapillary forceps biopsy (TPB) or EUS‐FNAB according to the characteristics of suspected MBS. Consecutive patients diagnosed with suspected MBS with obstructive jaundice and/or cholangitis were enrolled prospectively. ERCP with intraductal ultrasonography (IDUS) and TPB were performed as initial diagnostic procedures. Based on the results of imaging studies and IDUS, all MBS were classified as extrinsic or intrinsic type. If the malignancy was not confirmed by TPB, EUS‐FNAB for extrinsic type or second TPB for intrinsic type was performed. Among a total of 178 patients, intrinsic and extrinsic types were detected in 88 and 90 patients, respectively. The diagnostic accuracy of first TPB was significantly higher in the intrinsic than in the extrinsic type (81.8% vs. 67.8, P = 0.023). In 33 patients with extrinsic type and negative for malignancy on first TPB, the diagnostic accuracy of EUS‐FNAB was 90.9%. In 19 patients with intrinsic type and negative for malignancy on first TPB, the diagnostic accuracy of second TPB was 84.2%. The diagnostic accuracies of the combination of initial TPB with EUS‐FNAB and second TPB were 96.7% and 96.6%, respectively. A diagnostic approach using EUS‐FNAB or TPB according to the origin of MBS is considered effective to improve the diagnostic accuracy of MBS with negative for malignancy on first TPB. (Clinical trial registration number: UMIN000016886).