The diagnoses of hepatocellular carcinoma (HCC) are mostly made at advanced stage, which is associated with unfavorable prognosis and suboptimal survival. While dual-tracer PET/CT (dt-PET/CT) and gadoxetic acid-enhanced MRI are effective in detecting liver lesions, diagnostic performance of gadoxetic acid-enhanced MRI in identifying small HCC lesions compared with dt-PET/CT remains unclear. Here, we compare the sensitivity and specificity of each imaging modality to diagnose HCC. Gadoxetic acid-enhanced MRI has higher sensitivity in detecting HCC lesions than using dt-PET/CT, especially in smaller HCC lesions. Thus, gadoxetic acid-MRI could provide clinical value in the early diagnosis of HCC.