Abstract Background Transbronchial biopsy for peripheral pulmonary lesions is generally performed under X-ray fluoroscopy. Virtual bronchoscopic navigation (VBN) is a method in which virtual images of the bronchial route to the lesion are produced based on CT images obtained before VBN, and the bronchoscope is guided using these virtual images, improving the diagnostic yield of peripheral pulmonary lesions. VBN has the possibility of eliminating the need for X-ray fluoroscopy in the bronchoscopic diagnosis of peripheral lesions. To determine whether VBN can be a substitute for X-ray fluoroscopy, a randomized multicenter trial (non-inferiority trial) was performed in VBN and X-ray fluoroscopy (XRF) -assisted groups. Methods The non-inferiority margin in the VBN-assisted group compared with the XRF-assisted group was set at 15%. The subjects consisted of 140 patients with peripheral pulmonary lesions with a mean diameter > 3 cm. In the VBN-assisted group, the bronchoscope was guided to the lesion using a VBN system without X-ray fluoroscopy. In the XRF-assisted group, the same bronchoscope was guided to the lesion under X-ray fluoroscopy. Subsequently, in both groups, the lesion was visualized using endobronchial ultrasonography with a guide sheath (EBUS/GS), and biopsy was performed. In this serial procedure, X-ray fluoroscopy was not used in the VBNA group. Results The subjects of analysis consisted of 129 patients. The diagnostic yield was 76.9% (50/65) in the VBN-assisted group and 85.9% (55/64) in the XRF-assisted group. The difference in the diagnostic yield between the two groups was -9.0% (95% confidence interval: -22.3% ~ 4.3%). The non-inferiority of the VBN-assisted group could not be confirmed. The rate of visualizing lesions by EBUS was 95.4% (62/65) in the VBN-assisted group and 96.9% (62/64) in the XRF-assisted group, being high in both groups. Conclusions On EBUS/GS, a bronchoscope and biopsy instruments may be guided to the lesions using VBN without X-ray fluoroscopy, but X-ray fluoroscopy is necessary to improve the accuracy of sample collection from lesions. During transbronchial biopsy for peripheral pulmonary lesions, VBN cannot be a substitute for X-ray fluoroscopy. Trial registration UMIN-CTR (UMIN000001710); registered 16 February 2009.