Neisseria meningitidis is a Gram-negative bacterium frequently associated with invasive diseases with high mortality. Although its natural reservoir is the human nasopharynx, in recent years there have been increasing reports of isolation of this agent in the anorectal mucosa, mainly in men who have sex with men (MSM). We present the case of an HIV-positive MSM who consulted for urethritis and primary syphilis, in which N. meningitidis was isolated in an anorectal specimen. He was treated empirically with ceftriaxone and azithromycin, and a post-treatment control culture was negative. Despite the increase in anogenital infections and colonization by N. meningitidis, its role is unknown as a genital pathogen and in the transmission of other infections and the need for specific therapeutic regimens.