A recently weaned, stranded, male northern elephant seal (Mirounga angustirostris) pup that had been undergoing rehabilitation was found severely obtunded with hyponatremia, hypokalemia, hypochloremia, and hypophosphatemia after a history of intermittent regurgitation. The animal was euthanatized, and gross postmortem findings included multifocal abscessation affecting brain, spleen, kidney, muscle, and subcutaneous tissue. Scedosporium apiospermum and mixed bacteria were cultured from brain, kidney, and subcutaneous tissue. Histopathologic examination revealed multiple fungal granulomas of variable size in the kidneys, brain, liver, and skeletal muscle. This is the first report of S. apiospermum infection associated with lesions in a marine mammal.