Mucoceles are benign lesions of the oral cavity that develop as a result of retention or extravasation of mucous material from minor salivary glands. Congenital mucoceles are very rare. These lesions in newborns may interfere with breastfeeding and may even compromise respiratory function. A patient with a congenital mucocele diagnosed by prenatal ultrasound screening showing a cystic lesion of the tongue is presented herein. The physical examination, lesion evolution and imaging are described, together with the surgical management, histopathology and two-year follow-up. Early clinical assessment, differential diagnosis and magnetic resonance imaging allow clinicians to diagnose and treat this rare congenital condition with surgery in early infancy.