HIV is associated with disruptions in cognition and brain function. Marijuana use is highly prevalent in HIV but its effects on resting brain function in HIV are unknown. Brain function can be characterized by brain activity that is correlated between regions over time, called functional connectivity. Neuropsychiatric disorders are increasingly being characterized by disruptions in such connectivity. We examined the synergistic effects of HIV and marijuana use on functional whole-brain network organization during resting state. Our sample included 78 adults who differed on HIV and marijuana status (19 with co-occurring HIV and marijuana use, 20 HIV-only, 17 marijuana-only, and 22 controls). We examined differences in local and long-range brain network organization using eight graph theoretical metrics: transitivity, local efficiency, within-module degree, modularity, global efficiency, strength, betweenness, and participation coefficient. Local and long-range connectivity were similar between the co-occurring HIV and marijuana use and control groups. In contrast, the HIV-only and marijuana-only groups were both associated with disruptions in brain network organization. These results suggest that marijuana use in HIV may normalize disruptions in brain network organization observed in persons with HIV. However, future work is needed to determine whether this normalization is suggestive of a beneficial or detrimental effect of marijuana on cognitive functioning in HIV.