A female, captive bred, juvenile swell shark (Cephaloscyllium ventriosum) was observed swimming in tight circles and rolling. Radiographs and computed tomography of this individual revealed extensive cartilage mineralization of the skull and cranial cervical vertebrae compared with diagnostic images of clinically healthy conspecifics. Gross necropsy and histopathologic examination revealed ossification and fibrosis of the cartilaginous matrix of the skull and cervical vertebrae with deep invasion by a pigmented hyphal fungus. There was no growth on fungal culture, but fungal polymerase chain reaction identified a DNA sequence compatible with Exophiala sp. (99%). Radiographs and computed tomography were helpful to determine a prognosis and course of action for this individual. This case emphasizes the need to include fungal infections as a differential diagnosis when evaluating elasmobranchs with abnormal swimming behaviors and mineralization of the skeletal structures.