A congenital midline cervical cleft (CMCC) is a rare anomaly. Less than 100 cases report in English literature have been reported. This failure is presented at birth and in most cases is treated in the first months of life. We report an unusual case of a 14-year-old girl with untreated CMCC, which was misdiagnosed as thyroglossal duct cyst. The patient also presented rare congenital heart disease. In this case report we discuss the clinical presentation, diagnosis and surgical treatment. The aim of this case report is to draw attention to very rare case of patient with misdiagnosed CMCC.