Urogenital infections caused by Neisseria meningitidis (Nm) are increasing globally, yet the prevalence, antimicrobial resistance profiles, and transmission dynamics of Nm in men who have sex with men (MSM) remain poorly defined. We conducted an oropharyngeal carriage study in 174 MSM attending a London sexual health clinic in 2023, prior to the implementation of 4CMenB vaccination and doxycycline post-exposure prophylaxis (doxyPEP). Nm was detected in 21.26% of participants, with carriage significantly associated with throat gonorrhoea, consistent with frequent co-colonisation. Whole-genome sequencing identified diverse lineages, including hyperinvasive clonal complexes (CC)11 and CC4821, and revealed widespread tetracycline resistance: 43% of isolates carried either a conjugative tet(M) plasmid or chromosomal tet(B) efflux locus. These findings indicate that MSM represent an important reservoir of tetracycline-resistant Nm, with the potential amplification of this phenotype following doxyPEP implementation, underscoring the need for genomic surveillance of Neisseria species in sexual networks.