Hepatocellular carcinoma (HCC) is a common malignancy with high mortality, especially in HCC patients with brain metastases (BMS). However, few studies have investigated the risk factors for BMS among HCC patients based on large-scale population. The study involved clinical data of 36,091 patients who met the inclusion criteria from the SEER database, from 2004 to 2016. Univariate analysis and multifactor logistics regression analysis was used to analyze risk factors affecting BMS among HCC patients. This study revealed that BMS occurred in 108 of 36,091 patients, with an incidence of 0.33%. Median survival was 7 months for patients with BMS, but 12 months for patients without BMS. Univariate analysis showed that pathological low differentiation and undifferentiation, lymph node metastasis, no surgical treatment, and no chemotherapy and radiotherapy increased risk of BMS (P < 0.05). Multivariate analysis suggested that no surgical treatment and no chemotherapy or radiotherapy were independent risk factors for BMS (P < 0.001). Our findings highlighted that the independent risk factors for BMS were no surgical treatment, no chemotherapy, and no radiotherapy.