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Asymptomatic carriers are a likely source of transmission of Neisseria meningitidis to close contacts who are placed at a higher risk for invasive meningococcal disease (IMD). Although N. meningitidis ciprofloxacin-resistance is rare, there have been an increase in the reports of resistant isolates mainly in patients diagnosed with IMD, and little is known about the N. meningitidis ciprofloxacin-resistance in the carrier populations. We performed a pharyngeal carriage study during a 2017 military setting outbreak in Peru, caused by a ciprofloxacin-resistant N. meningitidis B. The isolates analysed came from two hospitalized cases and six asymptomatic carriers. Whole-genome sequence-based analysis was performed and showed that strains carrying the Thr 91 Ile mutation, in the gene encoding for subunit A of DNA gyrase ( gyr A), were responsible for the fluoroquinolone resistance (MICs ≥0.256 µg ml -1 ) and were closely related to highly virulent strains from France, Norway and the UK. Phylogenetic analysis of the gyr A gene revealed that likely these Peruvian isolates acquired resistance through horizontal gene transfer from Neisseria lactamica . Our study provides evidence for the emergence and propagation of ciprofloxacin-resistant N. meningitidis B from asymptomatic carriers, and recommends the introduction of serogroup B vaccines for high-risk populations.