Basal cell nevus syndrome (BCNS) is an autosomal dominant condition caused most often by a loss-of-function mutation in the Patched-1 (PTCH1) gene. It is characterized by the development of varied benign and malignant tumors, including numerous cutaneous basal cell carcinomas (BCCs). The PTCH1 gene is integral in hair follicle development and loss of function mutation may lead to BCCs with an infundibulocystic histopathology in BCNS patients. Few studies have described the histopathological features of BCCs in BCNS. The recognition of these histopathologic features by dermatologists, dermatopathologists, and others caring for children will allow earlier and more effective identification of BCNS. We performed a retrospective analysis of 25 BCCs in 11 patients aged 5 to 19 years with BCNS and evaluated the histopathologic features on hematoxylin-eosin-stained sections. Our study found that 80% of BCCs in BCNS patients occurred on the head and neck with 64% of the specimens demonstrating infundibulocystic differentiation. Infundibulocystic differentiation is a common finding in BCCs found in BCNS. The finding of cutaneous neoplasms consistent with BCC with infundibulocystic differentiation in children is common in pediatric patients with BCNS and can be considered to be an early marker of the disorder, prompting further clinical investigation.