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Abstract Resolving the phylogenetic relationships of early amniotes, in particular stem reptiles, remains a difficult problem. Three‐dimensional morphological analysis of well‐preserved stem‐reptile specimens can reveal important anatomical data and clarify regions of phylogeny. Here, we present the first thorough description of the unusual early Permian stem reptileBolosaurus major, including the first comprehensive description of a bolosaurid braincase. We describe previously obscured details of the palate, allowing for insight into bolosaurid feeding mechanics. Aspects of the rostrum, palate, mandible, and neurocranium suggest thatB. majorhad a particularly strong bite. We additionally foundB. majorhas a surprisingly slender stapes, similar to that of the middle Permian stem reptileMacroleter poezicus, which may suggest enhanced hearing abilities compared to other Paleozoic amniotes (e.g., captorhinids). We incorporated our new anatomical information into a large phylogenetic matrix (150 OTUs, 590 characters) to explore the relationship of Bolosauridae among stem reptiles. Our analyses generally recovered a paraphyletic “Parareptilia,” and found Bolosauridae to diverge after Captorhinidae + Araeoscelidia. We also includedB. majorwithin a smaller matrix (10 OTUs, 27 characters) designed to explore the interrelationships of Bolosauridae and found all species ofBolosaurusto be monophyletic. While reptile relationships still require further investigation, our phylogeny suggests repeated evolution of impedance‐matching ears in Paleozoic stem reptiles.