A significant swelling was seen in the floor of the mouth of a newborn girl. The girl could only drink with difficulty. On examination, a soft-elastic swelling was seen beneath the tongue. Ultrasonography and MRI showed a mass located above the hyoid bone. Upon the initial differential diagnosis of a dermoid cyst, an enucleation of the lesion was performed. Histopathological examination suggested a branchiogenic cyst or a digestive duplication cyst. Given the inconclusiveness of additional diagnostic examination, the lesion was diagnosed as a developmental cyst. Six months after enucleation, the infant girl’s tongue motility was not restricted and there were no indications of a recurrence. This rare case illustrates the variety in differential diagnosis and the limitations of additional diagnostic examination.