Neanderthals are among the best studied and yet most enigmatic fossil human groups with aspects of their anatomy and functional morphology remaining poorly understood. We present the first anatomical reconstruction of the Neanderthal cartilaginous Eustachian tube (CET), a vital component of the upper respiratory tract and nexus for the middle ear and postnasal airway. The Eustachian (auditory, pharyngotympanic) tube, comprised of a bony and cartilaginous (CET) portion, is integral to normal physiological functions such as middle ear aeration and pressure equilibration. Findings indicate that Neanderthal tubal morphology may have predisposed them to high rates of middle ear disease (otitis media [OM]). In living humans, mechanical CET dysfunction underlies OM in infants and young children, with sequelae including hearing loss, meningitis, and pneumonia. Despite proven linkage of CET malfunction with OM, the role of CET morphology in Neanderthal health and disease remains unstudied. We reconstructed Neanderthal CET morphology, comparing their crania to a modern human growth series. Methods included geometric morphometrics and univariate measures among Procrustes‐fitted coordinates. Results showed Neanderthal adults exhibiting primitively tall and narrow nasopharynges with infant‐like horizontal CET and choanal orientation. As horizontal CET orientation is associated with increased OM incidence in infants and children until around age six, its appearance in Neanderthal adults strongly indicates persistence of high OM susceptibility at this time. This could have compromised fitness and disease load relative to sympatric modern humans, affecting Neanderthals' ability to compete within their ecological niche, and potentially contributing to their rapid extinction. Anat Rec, 302:2109–2125, 2019. © 2019 American Association for Anatomy