Cistecephalidae is a relatively basal clade of dicynodonts, well-nested within emydopoids, and known to have multiple adaptations to a fossorial lifestyle. In recent years cistecephalid taxonomic diversity has been progressively increasing and important insights into the osteology, soft-tissue anatomy, and paleobiology of the clade have improved considerably. Here we describe a new genus and species of a cistecephalid from the Chiweta Beds (Northern Malawi, Wuchiapingian), a yet inadequately sampled area of Karoo sediments. Due to the minute dimensions and delicate nature of specimen PK-16-1, we have utilized, propagation phase-contrast synchrotron X-ray micro-computed tomography, revealing conspicuous contrast between rock matrix and bone and allowing reconstruction of its cranial osteology in great detail. PK-16-1 is here recognized as a new genus and species based on various autapomorphies, such as the presence of an atrophied preparietal and the presence of convergent crests along the pila antoticae. We performed a phylogenetic analysis in which we recovered PK-16-1 in a clade with Kembawacela and Cistecephalus united, among other characters, by a strongly embayed rostrum notch. Furthermore, the anatomical resolution obtained allowed us to reconstruct the osseous labyrinth, the paths for several nerve branches, arteries and veins for the first time in cistecephalids, and we develop new hypotheses for their paths and nomenclature for dicynodonts. We found remarkable resemblance in the brain endocast of PK-16-1 and another cistecephalid, Kawingasaurus, which is considerably distinct from other dicynodonts.