Human immunodeficiency virus (HIV) has continuously been considered a scourge in Indonesia. Negative societal stance might be attributed to the poor biological, psychological, and emotional knowledge of HIV. Here we aimed to demonstrate the level of knowledge, stigma, and barriers for accessing HIV services. We conducted a cross-sectional survey in December 2019 in Kemayoran District, Jakarta, Indonesia. The survey consisted of a demographic section, HIV-Knowledge Questionnaire 18, and Stigma Questionnaires. An in-depth interview was conducted with eight subjects representing high-risk HIV and healthcare professionals; in-vivo and thematic analysis were employed. Overall, 83 respondents participated, 50.6% male, and 61.7% aged 26-45 years old. Instrumental, symbolic, and civility stigma were significantly higher in 25.9%, 19.8%, and 17.3% of samples, respectively. Stigma was associated with HIV knowledge (λ: 0.887, df: 3, partial η2: 0.113), and high knowledge level decreased the odds of instrumental stigma (OR: 0.292, 95% CI 0.095-0.900, p<0.05). Fear of discrimination and limited information was identified as intrinsic factors, while media portrays HIV and extraneous screening hours as extrinsic factors. The knowledge on HIV is still low at the community level in the Indonesian capital, which correlates to higher stigma and inhibits the high-risk population from accessing HIV medical services.