Extra-mammary Paget’s disease (EMPD) is a rare epithelial adenocarcinoma occurring in apocrine-gland rich areas of the body. Primarily a dermatologic condition, there are multiple methods of treatment with a major barrier being high rates of recurrence with topical therapies. This case report presents a 61-year-old man with excision-resistant primary invasive EMPD to his bilateral groin regions. The patient had biopsy-confirmed disease following 2 years of symptoms. Thorough workup did not identify any underlying associated malignancy. He was managed surgically in the first instance with wide local excision, but recurrently identified close or involved margins necessitated re-excision and he eventually proceeded to complete scrotectomy with split thickness skin graft reconstruction. Despite the radical nature of his surgical management, adequate oncological clearance was not achieved and he went on to receive topical therapy to targeted areas. This case illustrates the difficulties managing an invasive and cryptic form of a rare cutaneous malignancy, and methods employed by multiple specialty teams to investigate and manage this disease.