Madrynornis mirandus, one of the few fossil penguins known from a nearly complete articulated skeleton, represents a key taxon for understanding the stem-crown transition in penguins. Despite the wealth of morphological character data preserved in the holotype specimen, the phylogenetic placement of this early late Miocene taxon has remained controversial. Reexamination of the Madrynornis mirandus holotype provides support for placement within the penguin crown clade. However, this placement is highly sensitive to the molecular signal and Madrynornis falls just outside the crown clade when molecular data are excluded. The neuroanatomy of Madrynornis shares many derived features with extant penguins, including an airencephalic brain shape, highly reduced bulbus olfactorius, and absence of an interaural pathway. However, the brain endocast differs from all surveyed extant species in that the eminentia sagittalis (wulst) is less caudally expanded, the tectum opticus is relatively less developed, and the flocculus is stouter and more laterally disposed. The cranial osteology and reconstructed jaw myology of Madrynornis suggest a primarily piscivorous diet, which likely characterizes the clade uniting Madrynornis, Inguza, Eudyptula, and Spheniscus.