Hamartomas are disorganized but benign masses composed of cells indigenous to the involved site. They have been reported in almost all organs but are rare in the head and neck region, especially the pharynx. We describe the case of a six-month-old male infant who presented with acute respiratory symptoms due to a pedunculated polypoid mass arising from his left palatine tonsil. He underwent a tonsillectomy and removal of the polyp after initial stabilization. Histopathological examination showed features consistent with hamartoma. The child had an uneventful recovery and follow-up after one year showed no evidence of recurrence. Our case highlights that rare benign lesions like hamartoma originating in the oral cavity, even in infants, can have such an acute presentation and should be considered in differential diagnosis.