Stigma and discrimination are major challenges faced by people living with HIV (PLWH), and stigma continues to be prevalent among PLWH. We conducted a cross-sectional study of 584 men who have sex with men (MSM) living with HIV between July 2018 and December 2020, designed to better understand which demographic and behavioral characteristics of MSM living with HIV in San Francisco, California are associated with experience of stigma, so that programs and initiatives can be tailored appropriately to minimize HIV stigma's impacts. This analysis was conducted with data from San Francisco AIDS Foundation (SFAF) encompassing services from multiple different locations in San Francisco. Data about the level of HIV-related stigma experienced were collected through a single question incorporated into programmatic data collection forms at SFAF as part of the client record stored in SFAF's electronic health record. We performed linear regression to determine the associations between self-reported experiences of HIV stigma and other characteristics among MSM living with HIV. HIV stigma was low overall among MSM living with HIV who are actively engaged in HIV care in San Francisco; however, it was significantly higher for the age groups of 13-29 years (adjusted risk difference (ARD): 0.251, 95% CI: 0.012, 0.489) and 30-49 years (ARD: 0.205, 95% CI: 0.042, 0.367) when compared to the age group of 50 years and older, as well as people who were homeless (ARD: 0.844, 95% CI: 0.120, 1.568), unstably housed (ARD: 0.326, 95% CI: 0.109, 0.543) and/or having mental health concerns (ARD: 0.309, 95% CI: 0.075, 0.544), controlling for race, injection history, and viral load. These findings highlight an opportunity to develop culturally, socially, and racially appropriate interventions to reduce HIV stigma among MSM living with HIV, particularly for younger men and those struggling with housing stability and/or mental health.