Data on Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) infections within HIV pre-exposure prophylaxis (PrEP) programs in low- and middle-income countries (LMICs) are limited. Our study reports the prevalence, anatomical distribution, and correlates of NG and CT infections within an HIV PrEP program in Hanoi, Vietnam. From January-December 2022, HIV PrEP program clients who were male at birth, ≥16 years old, reported ≥1 male sex partner in the prior 12 months, were enrolled. A questionnaire collected sociodemographics, sexual behaviors, and clinical data. CT/NG testing was performed on self-collected urine, rectal, and pharyngeal specimens. Multivariate logistic regression was used to identify factors associated with CT and NG infections. There were 529 participants enrolled, the median age was 25.1 years. The overall prevalence of CT or NG was 28.9% (153/529). The prevalence of NG was 14.3% and highest for pharyngeal infections (11.7%), while for CT, the prevalence was 20.4% and highest for rectal infections (14.0%). Symptoms in the prior week were reported by 45.8% (70/153) of those with CT or NG infections. Condomless anal sex (aOR= 1.98; 95% CI: 1.27, 3.08) and sexualized drug use in the prior 6 months (aOR= 1.68; 95% CI: 1.07, 2.65) were associated with CT/NG infections. Our study found a high prevalence of NG and CT infections, including pharyngeal and rectal infections, within an HIV PrEP program in Hanoi, Vietnam. The findings underscore the need for further research on CT/NG prevention and the development of evidence-based guidelines for CT/NG screening in HIV PrEP programs in LMIC settings.