The genus Macrocnemus is a member of the Tanystropheidae, a clade of non-archosauriform archosauromorphs well known for their very characteristic, elongated cervical vertebrae. Articulated specimens are known from the Middle Triassic of Alpine Europe and China. Although multiple articulated specimens are known, description of the cranial morphology has proven challenging due to the crushed preservation of the specimens. Here we use synchrotron micro computed tomography to analyse the cranial morphology of a specimen of the type species Macrocnemus bassanii from the Besano Formation of Monte San Giorgio, Ticino, Switzerland. The skull is virtually complete and we identify and describe the braincase and palatal elements as well the atlas-axis complex for the first time. Moreover, we add to the knowledge of the morphology of the skull roof, rostrum and hemimandible, and reconstruct the cranium of M. bassanii in 3D using the rendered models of the elements. The circumorbital bones were found to be similar in morphology to those of the archosauromorphs Prolacerta broomi and Protorosaurus speneri. In addition, we confirm the palatine, vomer and pterygoid to be tooth-bearing palatal bones, but also observed heterodonty on the pterygoid and the palatine.