Background: Although HIV prevalence in the general population of Mongolia remains low (<0.1%), infections are concentrated among key populations, particularly men who have sex with men (MSM) and transgender women (TGW). Regular monitoring of infection prevalence and associated risk behaviors is essential for early detection of epidemiological changes and timely response. Aim: To determine the prevalence of HIV and syphilis, assess levels of risk behaviors, and monitor trends among key populations. Materials and Methods: A simplified cross-sectional behavioral and biological surveillance survey was conducted in 2025, integrated with community center-based services in Ulaanbaatar and Darkhan. Non-probability sampling methods (venue-based, community center-based, online, and snowball sampling) were applied. HIV and syphilis infections were screened using rapid diagnostic tests, with confirmatory testing performed. Results: HIV prevalence was 0% among female sex workers (FSW), 6.1% among MSM, and 4.8% among TGW. Syphilis prevalence was 5.5% among FSW (decreasing trend), 12.6% among MSM (increasing trend), and 17.5% among TGW (highest). Coverage of community center-based prevention programs was 15.3% among FSW, 33.1% among MSM, and 64.6% among TGW, while condom use remained below 80% across all groups. Conclusion Although HIV prevalence in the general population remains low, concentrated transmission persists among MSM and TGW at approximately 5–6%. High levels of risk behaviors and insufficient coverage of prevention services indicate continued transmission risk. It is necessary to introduce pre-exposure prophylaxis (PrEP), strengthen STI prevention measures, and expand program coverage.