An elderly male with type 2 diabetes presented with a 2-month history of otalgia and severe headaches. He was diagnosed with malignant otitis externa (MOE) and was commenced on empirical treatment with oral ciprofloxacin. Pseudomonas is the most common cause of MOE. A baseline CT scan was undertaken that demonstrated skull base osteomyelitis (SBO) due to findings of bone erosion at the mastoid tip and an infiltrating soft tissue mass eroding the clivus. Eight weeks later, he returned with worsening and bilateral symptoms of otitis externa, hearing loss, temporomandibular pain and dysfunction. Worsening and now bilateral malignant otitis externa were confirmed with an MRI scan that also demonstrated a small fluid collection in his left temporal region. The collection was aspirated and grew scedosporium apiospermum. He was diagnosed with fungal SBO and was commenced on treatment with the antifungal voriconazole, with significant improvement in symptoms and radiological findings. Fungal osteomyelitis is more likely in immunosuppressed patients, particularly those with type 2 diabetes. Fungal aetiology should be suspected in patients with progressive symptoms, despite treatment. A microbiology diagnosis of fungal SBO or MOE can be challenging to obtain and can lead to diagnostic delay. A sampling of the external auditory canal can aid in diagnosing MOE; however, scedosporium may also be isolated as a commensal organism. Aspirations from accessible fluid collections, infratemporal fossa needle sample and bone biopsy can provide material for diagnosis. Scedosporium is a rare cause of disease in humans, however, fungal infections are increasing in humans, due to an increase in susceptible populations. Scedosporium apiospermum is a rare cause of SBO and should be considered in patients not responding to standard treatment.