Extra-genital Neisseria gonorrhoeae and Chlamydia trachomatis infections are associated with antimicrobial resistance and HIV acquisition. We analyzed data from a cohort of men who have sex with men (MSM) and transgender women followed quarterly for two years in Peru. Incident cases were defined as positive N. gonorrhoeae or C. trachomatis nucleic acid tests during follow-up. Repeat positive tests were defined as reinfection among those with documented treatment. We used generalized estimating equations to calculate adjusted incidence rate ratios (aIRRs). Of 404 participants, 22% were transgender. Incidence rates of rectal N. gonorrhoeae and C. trachomatis infection were 28.1 and 37.3 cases per 100 person-years, respectively. Incidence rates of pharyngeal N. gonorrhoeae and C. trachomatis infection were 21.3 and 9.6 cases per 100 person-years, respectively. Incident HIV infection was associated with incident rectal (aIRR = 2.43; 95% CI 1.66–3.55) N. gonorrhoeae infection. Identifying as transgender versus cisgender MSM was associated with incident pharyngeal N. gonorrhoeae (aIRR = 1.85; 95% CI 1.12–3.07) infection. The incidence of extra-genital N. gonorrhoeae and C. trachomatis infections was high in our population. The association with incident HIV infection warrants evaluating the impact of rectal N. gonorrhoeae screening and treatment on HIV transmission.