American Indian, Alaska Native, and Native Hawai'ian (hereafter referred to as Indigenous) people experience structural stressors borne from historic and ongoing systems of oppression and colonialization. Indigenous men who have sex with men (MSM) also contend with sexuality-based stressors related to their sexual behavior and/or identity. The confluence of these structural stressors is likely to compound their negative effects on health outcomes, including intimate partner violence (IPV), but there is little literature on IPV in this population. To begin to understand associations between compounding social stressors and IPV in this population, a 30-min online survey consisting of instruments previously validated in LGBT or Indigenous communities was targeted to Indigenous MSM using social media algorithms. Logistic regression models were fit to calculate adjusted associations between race- and sexuality-based structural stressors, theory-derived points of resiliency, and lifetime experience of physical, sexual, and emotional IPV. Respondents (n = 186) resided in 37 states and reported high levels of violence (physical: 50.3%, sexual: 40.7%, emotional: 83.2%). Anticipated stigma was significantly associated with a greater odds of reporting physical violence (AOR: 1.18). Reporting more instances of anti-Indigenous racism was significantly associated with reporting physical, sexual, and emotional IPV (AOR: 1.37, 1.29, 1.31, respectively). The results of this exploratory study suggest that Indigenous MSM experience high levels of IPV, and that structural stressors play a significant role as antecedents of violence. Anti-Indigenous racism should be a focal point of larger studies designed to elucidate points of intervention in this underserved population.