BACKGROUND: Caudal brainstem dysfunction associated with Chiari malformation type II (CM-II) is an important source of morbidity and mortality in neonates with myelomeningocele (MMC). OBSERVATIONS: Prenatal MMC repair has been shown to improve or even completely reverse the extent of hindbrain herniation (HH) associated with CM-II as well as reduce the incidence of hydrocephalus requiring CSF diversion, possibly leading to a reduction in CM-II-related symptoms in these children. Urgent CSF diversion and potential CM-II decompression surgery are typically the preferred treatments for infants demonstrating caudal brainstem dysfunction, although contemporary reports have described a decreased need for both CSF diversionary surgery and CM-II decompression following prenatal MMC repair. LESSONS: The authors present a unique case of a newborn demonstrating a rapid onset of severe caudal brainstem dysfunction despite imaging evidence of complete HH reversal following intrauterine MMC repair, highlighting the need for continued close monitoring of these infants despite satisfactory improvement in HH following fetal surgery. https://thejns.org/doi/10.3171/CASE24815.