Pharyngeal brain heterotopia is a congenital and generally biologically benign lesion. In contrast to brain heterotopia in the nose, the most common site of this lesion, brain heterotopia in the pharynx is very rare. Pharyngeal heterotopic tissue can be composed of various components, i.e., astrocytes, neurons, ependyma or choroid plexus, oligodendrocytes, retina, and, occasionally, neoplastic nodules. In contrast, nasal lesions are often only composed of astrocytes. We report a case of brain heterotopia in the pharyngeal region, diagnosed in a newborn female infant, causing serious respiratory distress. The infant underwent surgical excision of the lesion, and after 1 year of follow-up, she is recurrence-free. The mass, about 3 cm in diameter and showing no connection with encephalic structures, was characterized by numerous papillary structures and areas containing stellate-like or spindle cells focally forming nodules. Moreover, there was inflammatory infiltration, whereas mitoses, hemorrhages, and necroses were absent. Immunohistochemistry revealed a choroid plexus nature of the papillary formations (S-100, cytokeratins, transthyretin and vimentin-positive) and the presence of glial and neuronal cells in the remaining areas (glial fibrillary acidic protein, neuron-specific enolase, neurofilaments, synaptophysin, and S-100 positive). This case report confirms that the presence of choroid plexus is not uncommon and that pharyngeal brain heterotopia is usually benign.