Background: Hepatocellular Carcinoma (HCC) is a universal health problem responsible for 8.2% of all cancer deaths. Numerous risk factors were documented to be contributed to HCC development with viral hepatitis C ranking as the major predisposing factor in Egypt. The presence of a detectable amount of long noncoding RNAs (lncRNAs) in the circulation is linked to the development and spread of tumors. LncRNAs NBAT‐1 and FOXCUT expression levels were used as genetic markers for the detection of gastrointestinal tract cancers. We hypothesized that serum expression levels of NBAT‐1 and FOXCUT are new biomarkers for HCC that are related to laboratory and pathological markers. Patients and Methods: This study included 165 hepatitis C virus (HCV)‐related HCC Egyptian patients, 180 HCV‐infected noncancer patients, and 180 healthy controls, the serum expression levels of NBAT‐1 and FOXCUT were measured by using quantitative real‐time polymerase chain reaction. Results: This study's results include that medians (inter‐quartile range [IQRs]) of NBAT‐1 in HCC and HCV patients were (1.9 [0.87−4.94], 10.01 [7.34−13.29] respectively) which exhibited significantly higher expression than controls, while the medians (IQRs) of FOXCUT in HCC and HCV patients were (0.15 [0.04−0.52], 6.42 [2.49−10.10], respectively) that exhibited significantly lower expression than controls regarding HCC patients but significantly higher expression than controls regarding HCV patients. In comparing serum fold changes of NBAT‐1 and FOXCUT between HCC patients and HCV patients; we obtained significantly higher levels of target genes in HCV patients (p < 0.001) than in HCC patients. Also, a positive correlation was detected between NBAT‐1 and FOXCUT in HCC group (r = 0.262, p = 0.001) and in HCV group (r = 0.937, p < 0.001). Higher serum NBAT‐1 and FOXCUT were significantly associated with better clinical and laboratory data of the disease. Multivariate regression analysis showed that FOXCUT was an independent predictor for HCC among HCV patients (p < 0.001). Conclusion: Our study cited that NBAT‐1 and FOXCUT could be considered new diagnostic serum biomarkers for HCC on top of HCV.