Young black men who have sex with men (YBMSM) are disproportionately affected by HIV. Intersectional stigmas are associated with increased HIV vulnerability, and worse outcomes for YBMSM with HIV. YBMSM find sex partners through sexual networking apps, but stigma on apps has been poorly studied. We conducted cross-sectional analysis of 324 YBMSM seeking sex partners through apps to assess stigma experiences in eight dimensions compared to non-users (N = 150). We conducted detailed stratified analyses to identify granular stigma data. App users had higher median scores than non-users in perceived HIV discrimination, perceived HIV stigma, experienced sexual minority stigma, racial discrimination, and perceived homophobia. We demonstrate higher levels of intersectional stigmas among app users than non-users, but did not find an overall increase in stigma with increasing app use. Considering the prominent role of apps in YBMSM sexual networking, interventions that reduce stigma on apps are needed.