We herein present an extremely rare case of primitive neuroectodermal tumor originating in the penis. A 16-year-old male adolescent presented with painful penile swelling. Pathological, immunohistochemical and cytogenetical examinations of the specimens obtained from total penectomy confirmed the diagnosis of primitive neuroectodermal tumor. After total penectomy, the patient received adjuvant chemotherapy with ifosfamide-based regimen for 48 weeks. As a series of therapies, the patient underwent penile reconstruction surgery after completing adjuvant chemotherapy. The patient has not shown any evidence of recurrence for the 7 years after penile reconstruction surgery, and voiding function is completely normal. A favorable outcome was observed by multimodal therapy including aggressive resection for local control, intensive adjuvant chemotherapy, and penile reconstruction with cosmetic and functional success. Similar therapeutic approaches might be selected for children with primary malignant tumors of the penis.