Objectives: To identify factors associated with incarceration among women and examine the relationship between incarceration and human immunodeficiency virus (HIV)-related outcomes. Materials and Methods: We analyzed longitudinal data from 3324 women (2372 with HIV and 952 uninfected) from 2007 to 2016 in the Women's Interagency HIV Study, a U.S. cohort of women with and without HIV. Lifetime history of incarceration before first study visit was used as the outcome and then as a predictor for HIV outcomes and mortality. Using multivariable models, we assessed associations between socio-demographic, behavioral, and clinical characteristics and incarceration, and between incarceration and HIV outcomes, including mortality. Results: Overall, 1256 (38%) of women reported ever being incarcerated. Women who had a history of drug use had a 44% greater prevalence of incarceration compared with those who did not use drugs. Sexual minority women and women who experienced physical and sexual abuse had a 47% and 28%, respectively, greater prevalence of incarceration than heterosexual women and those not abused. For the 862 women with HIV and a history of incarceration, having an incarceration history was independently associated with less viral suppression (adjusted prevalence ratios = 0.95; confidence intervals [CI]:0.90-1.00 p = 0.04) and higher likelihood of death (adjusted hazard ratios = 1.39; CI:1.04-1.86 p = 0.03). Conclusions: Incarceration is common in this cohort and may put women with HIV at increased odds of worse HIV outcomes and mortality than those without a history of incarceration. Addressing the intersecting epidemics of HIV, substance use, and incarceration by providing needed treatment and resources and avoiding criminalization may improve health outcomes in vulnerable women with HIV.