We present a case of C1/C2 osteomyelitis secondary to malignant otitis externa complicated by atlantoaxial subluxation. This case is unique because surgical fixation of the spine was delayed, and despite clearance of the infection with antibiotics, the patient developed cervical myelopathy and required instrumented spinal fusion surgery. He presented with 1 month of fever, headache and worsening neck stiffness. An MRI of his cervical spine showed C1/C2 osteomyelitis with atlantoaxial subluxation. He was initially treated non-operatively with prolonged intravenous antibiotics and external immobilisation of his cervical spine. However, the first course of antibiotics failed, and he represented with a progression of his infection to the contralateral ear. He declined surgical intervention and completed a second course of antibiotics. Unfortunately, he eventually progressed to cervical myelopathy and subsequently underwent posterior C1 decompression with occipital to C4 instrumentation. There was no biochemical or bacterial culture evidence of infection at the time of the surgery. This case highlights the potential challenges in the management of cervical osteomyelitis-optimal duration of antibiotics is not supported by strong evidence and the clinician will therefore have to decide each treatment in the context of the patient. Spinal instability may still remain an issue after adequate treatment of the infection.