A hamartoma is a benign proliferation of typical mature cells specific to a particular anatomical site. In the oral cavity, they may occur as isolated cases or be associated with genetic syndromes. Oral-facial-digital syndrome type VI is a rare genetic disorder with an estimated incidence of one in 50,000-250,000 newborns. Here, we report a case of a 2-year-old boy diagnosed with oral-facial-digital syndrome type VI who was referred for evaluation of a bilateral and normochromic to slightly pinkish nodule on the lateral surface of the tongue. Clinically, the child presented hypotonia, low visual acuity, absence of oculocephalic reflex, delay in neuropsychomotor development, and polydactyly in the feet. Excisional biopsies of both sides of the tongue were performed using a 1.5 W high-power diode laser (wavelength of 980 nm), and histopathological analysis revealed abundant mature adipocytes predominantly arranged in lobules that mainly surrounded the minor salivary gland parenchyma. The surgical sites healed with no complications and the patient remains under follow-up for 10 months. Due to the limited literature on this syndrome and the frequent presence of tongue hamartomas in children, dentists need to be familiar with them.