Relatively complete ontogenetic series are comparatively rare in the vertebrate fossil record. This can create biases in our understanding of morphology and evolution, since immaturity can represent a source of unrecognized intraspecific variation in both skeletal anatomy and ecology. In the extinct marine reptile clade Ichthyopterygia, ontogenetic series were widely studied only in some Jurassic genera, while the ontogeny of the oldest and most basal members of the clade is very poorly understood. Here, we investigate cranial ontogeny in Mixosaurus cornalianus, from the Middle Triassic Besano Formation of the Swiss and Italian Alps. This small-bodied taxon is represented by a wealth of material from multiple size classes, including fetal material. This allows us to assess ontogenetic changes in cranial morphology, and identify stages in the ontogenetic trajectory where divergence with more derived ichthyosaurs has occurred. Early ontogenetic stages of Mixosaurus show developmental patterns that are reminiscent of the presumed ancestral (early diverging sauropsid) condition. This is prominently visible in the late fetal stage in both the basioccipital, which shows morphology akin to basal tubera, and in the postorbital, which has a triradiate head. The ontogenetic trajectory of at least some of the cranial elements of Mixosaurus is therefore likely still very akin to the ancestral condition, even though the adult cranium diverges from the standard diapsid morphology.