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Squamous cell carcinoma (SCC) accounts for 95% of penile malignant neoplasms. A subtype of SCC, named warty carcinoma (WC), is a morphologically distinct verruciform tumor with features of human papillomavirus (HPV)-related lesions. Descriptions of the behavior and histologic features of this tumor are scarce in the literature. The aim of this report is to analyze the clinicopathologic features and HPV deoxyribonucleic acid status in 60 SCCs and 11 WCs. The mean patient age was 46.5 ± 15.9 years for WC and 52.6 ± 12.4 years for SCC. No significant differences in age (p = 0.154) and clinical staging (T, p = 0.649; N, p = 0.497) between the two groups of tumors were found. When compared with SCCs, WCs exhibited less lymphatic embolization (p = 0.001), nodal metastasis (p = 0.019), and corpora cavernosa and corpus spongiosum infiltration (p = 0.040). Lymph node metastases were found in 34 of 60 SCC patients (56.7%) and in two of 11 WC patients (18.2%). No patients with WC tumors died of the disease compared with 19 of 60 (5-year specific survival, 66.0%) in the SCC group (p = 0.032). HPV deoxyribonucleic acid was more likely to be associated with WC (five of 11, 45.5%) than SCC (16 of 60, 26.7%), although significance was not reached (p = 0.209). The results suggest that WC is less aggressive and confers a better prognosis than typical SCC of the penis.