Dental implants are now the best treatment method to replace missing teeth. However, complications may necessitate further therapeutic interventions because of anatomic limitations and mistakes during surgical procedures. In this case report, a nasopalatine duct cyst (NPDC) due to implant placement was studied. After clinical and radiographic evaluation, unilocular radiolucency with disturbance to the nasopalatine canal was observed. Following that, flap elevation was performed. Subsequently, the cyst was enucleated, and the bone defect was filled with xenograft and further covered with a resorbable membrane. Histopathology results confirmed NPDC as the definite diagnosis. After six months, the defect was completely resolved.