Background: Enteric duplication cysts are congenital malformations that typically affect children in infancy, but can also affect adults. Rarely, these cysts can be complicated by malignancy. We present the first case of retroperitoneal duplication cyst that was complicated by malignancy transformation and managed by robot-assisted excision. Case presentation: A 64-year-old female with a history of a left-sided renal cyst presented with a 4-month history of abdominal pain and fatigue. MRI revealed a bilobed cyst, with components measuring 6.9 × 6.6 and 6.1 × 6.9 cm, which had grown since previous imaging, and hemorrhage in some portions of the cysts, as well as cystic wall enhancement, suggesting a possible malignancy. The patient consented to a robot-assisted partial (possible radical) nephrectomy. During the procedure, the cystic structure appeared to have grown since imaging, was intimately associated with the hilum, and had a complex vasculature, which prompted us to perform a radical nephrectomy. Grossly, the specimen consisted of a 14.8 cm cystic structure at the superior portion of the kidney, but was not contained within the renal parenchyma. Histologically, the internal mucosa of the cyst showed columnar epithelium with high-grade dysplasia and carcinoma in situ with focal individual cell infiltration into the superficial portion of the inferior part of the cyst. The patient saw a medical oncologist and was instructed to follow up with quarterly imaging to assess for disease progression. Conclusion: Enteric duplication cysts are uncommon entities that can occur in various locations in the body, causing a wide spectrum of symptoms, and are rarely complicated by malignancy transformation. Robot-assisted surgical resection is an option that we have shown to be effective in managing these patients.