Otogenic skull base osteomyelitis (OSBO), a severe infection originating from the dissemination of infection from the middle or external auditory canal into the osseous structures of the skull base, is frequently caused by predominant causative agents such as Pseudomonas aeruginosa. Conventional microbiological cultures exhibit limitations, particularly following antibiotic pre-treatment or in cases involving fastidious microorganisms, frequently resulting in diagnostic delays. Fusobacterium necrophorum represents an exceedingly uncommon aetiological agent of OSBO, especially when compounded by bilateral involvement and intracranial dissemination. The advancement of molecular diagnostic techniques has witnessed the burgeoning application of metagenomic next-generation sequencing (mNGS) in the etiological identification of culture-negative or diagnostically challenging infections. Possessing inherent high-throughput and unbiased attributes, it furnishes a novel modality for the expeditious and precise delineation of causative pathogens. This paper presents a case report detailing an exceptionally rare instance of bilateral otogenic skull base osteomyelitis complicated by meningitis, attributed to Fusobacterium necrophorum. Imaging studies in this particular case revealed osseous erosion within specific regions of the skull base. Aetiological investigation, conducted via plasma mNGS, successfully pinpointed Fusobacterium necrophorum as the pathogenic culprit. This facilitated the administration of effective targeted antibiotic therapy, leading to clinical amelioration. This study endeavours, through the exposition of this case, to explore the significant utility of mNGS in the aetiological diagnosis of intricate skull base infections and its pertinent clinical implications, thereby offering valuable insights and guidance for the diagnosis and management of analogous clinical scenarios.