Basal cell nevus syndrome is caused by mutations in the Sonic hedgehog pathway and characterized by early-onset basal cell carcinoma. The features of basal cell carcinoma in basal cell nevus syndrome compared with sporadic basal cell carcinoma have not been explored. This study is a retrospective study of patients with basal cell nevus syndrome in two medical centres in Taiwan from 1991 to 2021 and patients with sporadic basal cell carcinoma excised from 2015 to 2020. An analysis of 18 patients with basal cell nevus syndrome showed an older mean age at the first diagnosis of basal cell carcinoma (37.5 years) than reported in Western countries. The majority of basal cell carcinomas were located in the head and neck region (80.7%), with nodular BCC being the most common tumour type (47.0%). Compared with sporadic basal cell carcinomas, basal cell carcinomas in basal cell nevus syndrome patients occurred more frequently on the scalp (34.7% vs 6.1%, p < 0.001). In addition, the superficial type of basal cell carcinoma was more likely to be seen in basal cell nevus syndrome (24.7% vs 10.4%, p < 0.001). The limitations were that some features of the basal cell nevus syndrome patients might not have been present yet at the time of examination or they did not receive thorough screening. In conclusion, the distinct features of basal cell carcinomas in basal cell nevus syndrome patients have important implications for the prevention, diagnosis, and management of basal cell carcinoma in basal cell nevus syndrome patients.