Determination of the major serogroups is an important step for establishing a vaccine programme and management strategy targeting Neisseria meningitidis. From April 2010 to November 2016, a total of 25 N. meningitidis isolates were collected in South Korea, in collaboration with the Korean Society of Clinical Microbiology. Among isolates, 19 isolates were recovered from blood and/or cerebrospinal fluid (CSF) in 46 patients who suffered from invasive meningococcal disease (IMD), and six isolates were found in sputum or the throat. The most common serogroup was serogroup B (overall, 36%, n = 9/25; IMD, 37%, n = 7/19), which was isolated in every year of the research period except for 2011. There were five serogroup W isolates recovered from patients in military service. W was no longer isolated after initiation of a vaccine programme for military trainees, but serogroup B caused meningitis in an army recruit training centre in 2015. In MLST analysis, 14 sequence types were found, and all isolates belonging to W showed the same molecular epidemiologic characteristics (W:P1.5-1, 2-2:F3-9:ST-8912). All isolates showed susceptibility to ceftriaxone, meropenem, ciprofloxacin, minocycline, and rifampin; however, the susceptibility rates to penicillin and ampicillin for isolates with W and C capsules were 22% and 30%, respectively.