Petalichthyid and “acanthothoracid” placoderms have taken pivotal positionsin the debate on placoderm—and, by extension, jawed vertebrate—relationships owing to perceived similarities with the jawless vertebrates. Neurocranial characters are integral to current hypotheses of early gnathostome relationships. Here, we describe the three-dimensionally preserved neurocranial anatomy of the petalichthyid placoderm Ellopetalichthys scheii, from the Middle Devonian (early Eifelian) of Ellesmere Island, Canada. Using X-ray computed microtomography, we generated three-dimensional reconstructions of the endocranial surfaces, orbital walls, and cranial endocavity. These reconstructions verify the absence of a crus commune of the skeletal labyrinth and the complex shape of the petalichthyid endolympathic duct. Details of the craniothoracic joint and occipital musculature fossae help resolve the problematic comparative anatomy of the occipital surface of petalichthyids. These new data highlight similarities with arthrodire placoderms, consistent with older hypotheses of a sister-31group relationship between petalichthyids and that clade.