Men who have sex with men (MSM) in Western urban areas have seen substantive decreases in new diagnoses of HIV infection. This paper explores whether such declines are present among MSM and transgender women (TGW) in Southeast Asia and discusses implications for HIV policies and programming. A scoping review was conducted of scientific publications and selected documents regarding the spread of HIV infection among MSM and TGW in major urban centres of the Association of Southeast Asian Nations (ASEAN) region. Continued high HIV prevalence and incidence among MSM are found in integrated behavioural and biological surveillance (IBBS) and research studies. HIV prevalence among MSM under IBBS decreased only in Bangkok from 28.6% in 2014 to 10.3% in 2018, whereas it was increasing in Kuala Lumpur, Ho Chi Minh City, Vientiane, and Phnom Penh. HIV/AIDS case reports regarding new HIV infection diagnoses among MSM have started to decrease in Singapore since 2011 and have been plateauing in Metropolitan Manila since 2017. Where data were available, it was found that HIV prevalence among TGW was high and if IBBS was conducted, it was increasing. HIV prevalence among TGW under IBBS in Jakarta had risen to 34.0% (2015) and 14.0% (2019) in Phnom Penh. These findings suggest that most ASEAN member states have so far failed to effectively implement and scale-up scientifically proven biomedical HIV prevention measures and counter stigma and discrimination that impedes access to appropriate HIV prevention and treatment services for MSM and TGW.