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Abstract Background Primary malignant melanoma of the female urethra is an exceedingly rare tumor. It represents 0.2% of all malignant melanomas. Divergent differentiation towards non-melanocytic lineages has not been reported in urethral melanoma. Case presentation We report a rare case of neuroendocrine differentiation in a large primary small cell malignant melanoma involving the urethra, in a 62-year-old lady, who presented with obstructive urinary symptoms. Clinical and radiological workup revealed a large urethral mass with liver and lymph nodal metastases. A biopsy was performed from the urethral and liver lesions which showed poorly differentiated tumor cells with small cell morphology and presence of melanin pigment. These cells were immunopositive for melanocytic and neuroendocrine markers. Ultrastructural examination showed presence of melanosomes and neurosecretory granules in the tumor cells. Conclusions Although malignant melanoma with neuroendocrine differentiation is exceptionally rare, it needs to be recognized among the other well-known variants of malignant melanoma.