Rectal duplication cysts are a rare entity, representing only 5% of alimentary tract duplications, with posterior rectal duplications being the most common. However, clinical presentations can vary significantly. We present a unique case of a 5-day-old female with an antenatally ruptured rectal duplication cyst associated with spina bifida and an ectopic kidney. The infant presented with a fleshy mass over the left gluteal region, and imaging revealed an ectopic left kidney and spina bifida. The preoperative diagnosis was complicated by the antenatal rupture of the cyst, which was confirmed intraoperatively and through biopsy. Surgical excision of the lesion was performed, and the postoperative recovery was uneventful. This case underscores the diagnostic challenges associated with ruptured rectal duplication cysts in the newborn period, highlighting that complete surgical excision is the preferred treatment to prevent further complications.