Hereby, we present a rare case of malignant transformation in a long-standing case of pseudoepitheliomatous keratotic and micaceous balanitis (PKMB), which typically affects older men. PKMB presents as whitish or silvery keratotic plaques on the glans and can remain stable for years, leading to potential confusion regarding its progression. The patient in this case experienced urinary obstruction due to tumorous ingrowth, prompting an investigation. Despite previous treatments, including fluorouracil (5-FU) and cryoablation, the lesion persisted, eventually growing in size and becoming malodorous. Initial biopsy showed PKMB without malignancy, but subsequent deeper biopsy revealed verrucous carcinoma. The patient underwent glansectomy and reconstruction with a full-thickness skin graft, achieving a disease-free state postoperatively. The paper underscores the importance of thorough investigation for malignancy in PKMB cases, the possibility of deeper malignancy missed by superficial biopsy, and the need for early diagnosis to enable organ-sparing treatments.