With the transition of HIV infection from an acute to a chronic disease after the introduction of antiretroviral medications, there has been an increased focus on long-term neurocognitive and other functional outcomes of HIV patients. Thus, we assessed factors, particularly history of a substance use disorder, associated with time to loss of measures of physical or mental independence among HIV-positive individuals. Data were obtained from the National NeuroAIDS Tissue Consortium. Kaplan-Meier and Cox proportional hazards regression analyses were used to estimate the time since HIV diagnosis to loss of independence, and to identify associated risk factors. HIV-positive participants who self-identified as physically (n = 698) or mentally (n = 616) independent on selected activities of daily living at baseline were eligible for analyses. A history of substance use disorder was associated with a higher hazard of loss of both physical and mental independence [adjusted hazard ratio (HR) = 1.71, 95% confidence interval (95% CI): 1.07-2.78; adjusted HR = 1.67, 95% CI: 1.11-2.52, respectively]. After adjusting for substance use disorder and other covariates, older age at diagnosis and female gender were associated with higher hazards of loss of both physical and mental independence, non-white participants had higher hazards of loss of physical independence, whereas participants with an abnormal neurocognitive diagnosis and fewer years of education had higher hazards of loss of mental independence. In summary, history of substance use disorder was associated with loss of measures of both physical and mental independence. The nature of this link and the means to prevent such loss of independence need further investigation.