The purpose of this study was to investigate the value of virtual tissue quantification (VTQ) of acoustic radiation force impulse elastography for the differential diagnosis of benign and malignant focal liver lesions (FLLs). Thus, a total of 134 FLLs in 134 patients were included. VTQ measurement was performed for each lesion in which the shear wave velocity (SWV) was measured. The difference in SWV and SWV ratio of FLL to surrounding liver between malignant and benign FLLs was evaluated, and the cutoff value was investigated. Receiver operating characteristic (ROC) curve was plotted to evaluate the diagnostic performance. A total of 134 lesions including 55 (41.0%) malignant FLLs and 79 (59.0%) benign ones were analyzed. The SWV of malignant and benign FLLs was 2.95 ± 1.00 m/s and 1.69 ± 0.89 m/s, respectively. Significant difference in SWV was presented between malignant and benign FLLs (p < 0.001). The SWV ratio of each FLL to the surrounding liver parenchyma was 1.83 ± 1.32 for malignant and 1.26 ± 0.78 for benign FLLs (p < 0.001). The area under the ROC curve in distinguishing malignant from benign lesions was 0.824 for SWV and 0.660 for SWV ratio. The cutoff value for differential diagnosis was 2.13 m/s for SWV and 1.37 for SWV ratio. The associated sensitivity and specificity were 83.3 and 77.9% for SWV and 59.6 and 77.3% for SWV ratio, respectively. In conclusion, VTQ provides quantitative stiffness information of FLLs and is helpful in the differential diagnosis between malignant and benign FLLs, particularly for the patients who are not candidates for contrast-enhanced imaging such as CT, MRI or contrast-enhanced ultrasound.