Abstract Background No updated data currently exist regarding Neisseria meningitidis carriage and genomic epidemiology among young Israeli adults. Methods Oropharyngeal swabs were collected from 1801 military recruits on the day of recruitment during 2019. Neisseria meningitidis was detected and identified by culture and quantitative polymerase chain reaction (qPCR). Confirmed isolates were serotyped by qPCR, and encapsulated strains underwent whole-genome sequencing. Risk factors for carriage were determined by analyzing focused questionnaires using uni- and multivariate models. Genomic typing was performed by means of core genome multilocus sequence typing. Results Carriage rates overall and of encapsulated strains were 20.1% and 6.7%, respectively. Genogroups B (49.2%) and Y (26.7%) were the most commonly encapsulated strains. Genogroups C, W, and X were scarce, and genogroup A was absent. The most notable clonal complexes (CCs) were CC23 (n = 30), CC32 (n = 16), and CC44/41 (n = 9). Carriage was significantly associated with smoking (odds ratio [OR], 1.82; 95% CI, 1.43–2.33) and boarding school attendance before recruitment (OR, 1.49; 95% CI, 1.14–1.96). Conclusions The prevalence of meningococcal carriage among young Israeli adults is high, compared with similar studies in other developed countries. This might be due to sociocultural characteristics including smoking and boarding school attendance during and after high school. The dominant genogroups and CCs found were compatible with those implicated in invasive disease in Israel.