Background Fibroblast activation protein (FAP) is commonly expressed in activated stromal fibroblasts in various epithelial tumours. Recently, 68 Ga-FAPI-04 has been used for tumour imaging in positron emission tomography/computed tomography (PET/CT). This study aimed to compare the diagnostic performances of 68 Ga-FAPI-04 PET/CT and 18 F-FDG PET/CT in hepatocellular carcinoma (HCC), and to assess factors associated with 68 Ga-FAPI-04 uptake in HCC. Materials and Methods Twenty-nine patients with suspiciously HCC who received both 18 F-FDG and 68 Ga-FAPI-04 PET/CT were included in this retrospective study. The results were interpreted by two experienced nuclear medicine physicians independently. The maximum and mean standardized uptake values (SUV max and SUV mean ) were measured in the lesions and liver background, respectively. The tumour-to-background ratio (TBR) was then calculated as lesion’s SUV max divided by background SUV mean . Results A total of 35 intrahepatic lesions in 25 patients with HCC were finally involved in the statistical analysis. 68 Ga-FAPI-04 PET/CT showed a higher sensitivity than 18 F-FDG PET/CT in detecting intrahepatic HCC lesions (85.7% vs . 57.1%, P = 0.002), including in small (≤ 2 cm in diameter; 68.8% vs . 18.8%, P = 0.008) and well- or moderately-differentiated (83.3% vs . 33.3%, P = 0.031) tumors. SUV max was comparable between 68 Ga-FAPI-04 and 18 F-FDG (6.96 ± 5.01 vs . 5.89 ± 3.38, P > 0.05), but the TBR was significantly higher in the 68 Ga-FAPI-04 group compared with the 18 F-FDG group (11.90 ± 8.35 vs . 3.14 ± 1.59, P < 0.001). SUV max and the TBR in 68 Ga-FAPI-04 positive lesions were associated with tumour size (both P < 0.05), but not the remaining clinical and pathological features (all P > 0.05). Conclusions 68 Ga-FAPI-04 PET/CT is more sensitive than 18 F-FDG PET/CT in detecting HCC lesions, and 68 Ga-FAPI-04 uptake is correlated mainly with tumour size.