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Background: Morganella morganii represents a ubiquitous motile, anaerobic gram-negative rod bacterium inhabiting the intestinal tract of reptiles, mammals, and a minority of humans as normal flora. M. morganii is associated with wound infections, septicemia, and urinary tract infections. It has a notably rare incidence in the pathogenesis of central nervous system (CNS) infections. To the best of the authors' knowledge, only 18 documented CNS infections caused by M. morganii have been reported in the literature. Case presentation: A 46 years old opium-addicted male presented to our emergency department with the chief complaint of severe headache. He underwent surgery with the diagnosis of an aneurysm. Six weeks later, he returned with a reduced level of consciousness. Clinical evaluations revealed hydrocephalous and bacterial meningitis, for which a cerebrospinal fluid (CSF) diversion was performed, and empirical antibiotic therapy was prescribed. Afterward, a CSF culture demonstrated the presence of M. morganii, prompting the antibiotics to be changed following an antimicrobial sensitivity test. Although the patient partially responded to treatment, he ultimately succumbed to M. morganii meningitis. Conclusion: Although delayed M. morganii CNS infection with post-micro-surgical aneurysm clipping is a rare phenomenon, its potential as a highly lethal agent of post-surgical meningitis demands the attention of clinicians.