Cutaneous leishmaniasis (CL) is one of the prevalent parasitic diseases in Iran principally caused by two species, Leishmania major and L. tropica. Here, we present a rare case of a congenital form of CL around the glans penis from the central part of Iran in 2017. A 24-yr-old male patient from the central part of Iran presented with biennial ulceration of the glans penis. Diagnostic methods included physical and preclinical examination, microscopic observation, leishmanin skin test (LST), and serological tests including direct agglutination test (DAT). Nested PCR and sequencing analysis were used on the positive smears for confirmation of CL and Leishmania species identification. The preclinical results were normal, and no anti-Leishmania antibodies were detected in the peripheral blood of the patient using DAT. In abdominal ultrasonography, the spleen and liver size were normal. LST was positive (≥5 mm) after 72 h, and a few amastigote forms of Leishmania sp. were demonstrated under light microscopy. L. major was confirmed using nested PCR and sequencing analysis. The patient responded to oral administration of miltefosine (2.5 mg/kg/d) for 28 days. To the best of our knowledge, genital CL due to L. major has not been previously reported from Iran.