Hair follicle nevus (HFN) is a rare, benign, follicular hamartoma that most frequently presents as a congenital nodule on the face. We experienced a rare case of HFN presenting as a solitary papule on the neck and compared cytokeratin 19 (CK19) expression of hair follicles in HFN and its differential diagnoses, including accessory tragus, cervical chondrocutaneous branchial remnants (CCBR) and trichofolliculoma. A 14-year-old boy presented with an asymptomatic 3-mm sized, skin-colored, soft, pedunculated papule on his right lower neck, and a 2-mm sized, red-colored, dome-shaped papule with bleeding tendency on his right upper neck. Histopathologically, the lower skin-colored papule showed many vellus hair follicles in the dermis and several sebaceous and eccrine glands connected to the hair follicle. Perifollicular stroma showed fibrous thickening. Diagnosis of HFN was established. The upper red-colored papule was histologically consistent with pyogenic granuloma. CK19, a useful marker for human hair follicle stem cells, was expressed in some of the hair follicles in HFN, accessory tragus and CCBR, but not in trichofolliculoma. Our results suggest that HFN, accessory tragus and CCBR may be spectrum hamartomas. In contrast, trichofolliculoma differs from HFN in that it is composed of hair follicles with abnormal hair cycle, and CK19 can be utilized to differentiate the two diseases.