Chlamydia trachomatis and Neisseria gonorrhoeae are among the most common sexually transmitted bacterial infections in the world. Data are limited, however, on the burden of extra-genital chlamydial and gonococcal infections among men who have sex with men and transgender women in Lima, Peru. Data were gathered from self-collected anal or pharyngeal swabs from participants in Lima, Peru, and analyzed via cross-sectional methods. Prevalence ratios for the association between extra-genital infection with socio-demographic and sexual behaviors were determined. Overall, 127 (32.8%) participants had anal or pharyngeal infections. On multivariate modeling, anal infection was positively associated with practicing both receptive and insertive anal sex, when compared to insertive alone (PR = 2.49; 95% CI = 1.32–4.71), and negatively associated with any antibiotic use in the prior three months (PR = 0.60; 95% CI = 0.39–0.91). Pharyngeal infection was negatively associated with age greater than 30 years compared to 18–30 years (PR = 0.54; 95% CI = 0.30–0.96), and positively associated with gender identity of transgender women (PR = 2.12; 95% CI = 1.20–3.73). This study demonstrates considerable burden of extra-genital chlamydial and gonococcal infections among men who have sex with men and transgender women in Lima, Peru.