A 7-month-old, male Magellanic penguin (Spheniscus magellanicus), housed in an outdoor exhibit, developed acute neurologic signs that progressed to death over 2 days. On gross examination, the bird had congested, edematous lungs, and cerebellar hemorrhage. Histologic examination identified granulomatous pneumonia and encephalitis, with thrombosis and eosinophilic, branching fungal hyphae that had invaded the meningeal vessel walls. Polymerase chain reaction identified the fungus in the brain as Rhizomucor pusillus, an uncommon cause of mucormycosis. This organism has previously been reported in respiratory, skeletal, and sino-orbital lesions of avian species. This clinical report describes meningoencephalitis associated with Rhizomucor pusillus in a penguin.