Serum tumor markers, including α-fetoprotein (AFP) and des-γ-carboxy prothrombin (DCP), are currently used in the diagnosis of hepatocellular carcinoma (HCC). There is, however, an aberrant increase in serum DCP in patients with obstructive jaundice, vitamin K deficiency or who are taking warfarin, resulting from a problem with the current methodology for measurement of this marker. This study aimed to elucidate the utility of a new biomarker, NX-PVKA, for early diagnosis of HCC. A total of 96 patients were included in the HCC group. The control group included 138 liver cirrhosis (LC) patients without HCC. Serum concentrations of conventional DCP, AFP, AFP-L3 and NX-PVKA were measured. The NX-PVKA ratio was calculated by dividing DCP by NX-PVKA. In patients not taking warfarin, the area under the curve values of DCP, NX-PVKA ratio, AFP and AFP-L3 were 0.715, 0.690, 0.737 and 0.654, respectively, confirming the clinical utility of these markers in detecting HCC. In cases with DCP > 35 mAU/mL in particular, a significant increase in the NX-PVKA ratio was observed in patients with HCC. In those cases, the cut-off value for the NX-PVKA ratio that was optimized by the receiver operating characteristic (ROC) curve was 1.15. In addition, the sensitivity and specificity for diagnosing HCC were 69.2% and 75.9%, respectively. Patients with HCC had higher NX-PVKA ratios compared to patients with LC taking warfarin (P = 0.063). These results suggest that, when used in combination with DCP, the NX-PVKA ratio is a promising novel marker for the detection of HCC.