Differentiating maxillary radiolucent lesions is challenging due to overlapping clinical and radiographic features. Nasopalatine cysts (NPCs), the most common non-odontogenic cysts, originate from epithelial remnants of the nasopalatine duct and typically appear in the anterior maxillary midline. In contrast, apical pathologies result from pulpal necrosis, leading to periapical abscesses, granulomas, or cysts. This case report describes a 32-year-old female with a symptomatic maxillary anterior lesion initially suspected to be endodontic in origin. However, clinical examination, pulp vitality tests, and cone-beam computed tomography (CBCT) confirmed an NPC diagnosis. This highlights the necessity of a systematic diagnostic approach integrating clinical assessment, imaging, and histopathology to distinguish NPCs from apical pathology. Early and accurate identification prevents unnecessary endodontic treatment and ensures optimal patient care.