Klebsiella variicola, a member of K. pneumoniae phylogroup, can cause severe infectious diseases. We report a case of K. variicola meningitis after neurosurgery. The bacterium was isolated from blood and cerebrospinal fluid, and bacterial species identification was carried out by using both matrix-assisted laser-desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF MS) and whole genome sequencing. Initially, the organism was misidentified as K. pneumoniae by VITEK®2; automated system in the clinical laboratory examination. The patient recovered with the combination of surgical drainage and antimicrobial treatment. To our knowledge, this is the first case report of post-surgical meningitis caused by K. variicola. As experienced in this case, the automated bacterial identification system popularly being used in the clinical laboratory might not be effective enough for bacterial species identification. The use of MALDI-TOF MS for microbial identification may be helpful to physicians for appropriate management of K. pneumoniae phylogroup infection.