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Central skull base osteomyelitis is a rare, life-threatening condition that can present with vague symptoms and may be missed on initial imaging. We describe a man in his 30s who presented to the emergency department with rapidly progressive neck pain and elevated inflammatory markers. CT imaging was normal, but MRI revealed right occipital condyle osteomyelitis. Blood cultures grew methicillin-resistant Staphylococcus aureus, with the source determined to be from his upper and lower limb furunculosis. Despite appropriate antibiotics, he developed cranial nerve deficits and hearing loss. This case highlights the limitations of CT and the importance of early MRI in suspected central skull base osteomyelitis to avoid diagnostic delay and reduce complications.