In Japan, several meningococcal disease outbreaks have recently been reported among adolescent dormitory residents of schools. However, little is known about meningococcal carriage dynamics in healthy individuals. The purpose of this study was to investigate the carriage rate over time and characteristics of Neisseria meningitidis strains among dormitory students. The survey was conducted twice between November 2018 and January 2019 for first- to third-year students (N = 376) in a medical school dormitory. The two surveys yielded carriage rates of 0.4% (one positive among 257 students) and 2.1% (two positives among 97 students, including 90 re-participants). No transmission or persistence of a specific strain was observed during the two months. A limited number of students had a history of potential risk behaviors for carriage, such as smoking (3.0% [6/202] aged ≥20 years and 5.2% [4/77] aged ≥20 years, respectively) and attending parties more than once a week (4.3% [11/257] and 2.1% [2/97], respectively). Two isolates were unencapsulated, consistent with asymptomatic participants.