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Background: Endobronchial ultrasound-guided transbronchial biopsy (EBUS-TBB) is used for the diagnosis of peripheral pulmonary lesions (PPLs), but the diagnostic yield is not adequate. Cone-beam computed tomography-derived augmented fluoroscopy (CBCT-AF) can be utilized to assess the location of PPLs and biopsy devices, and has the potential to improve the diagnostic accuracy of bronchoscopic techniques. The purpose of this study was to verify the contribution of CBCT-AF to EBUS-TBB. Methods: Patients who underwent EBUS-TBB for diagnosis of PPLs were enrolled. The navigation success rate and diagnostic yield were used to evaluate the effectiveness of CBCT-AF in EBUS-TBB. Results: In this study, 236 patients who underwent EBUS-TBB for PPL diagnosis were enrolled. One hundred fifteen patients were in CBCT-AF group and 121 were in non-AF group. The navigation success rate was significantly higher in the CBCT-AF group (96.5% vs. 86.8%, p = 0.006). The diagnostic yield was even better in the CBCT-AF group when the target lesion was small in size (68.8% vs. 0%, p = 0.026 for lesions ≤10 mm and 77.5% vs. 46.4%, p = 0.016 for lesions 10–20 mm, respectively). The diagnostic yield of the two study groups became similar when the procedures with a failure of navigation were excluded. The procedure-related complication rate was similar between the two study groups. Conclusion: CBCT-AF is safe, and effectively enhances the navigation success rate, thereby increasing the diagnostic yield of EBUS-TBB for PPLs.