Objective: To identify the neural markers of attention dysfunction in patients with HIV-associated neurocognitive disorder (HAND). Methods: Sixty participants, including 40 HIV-infected adults (half with HAND) and 20 demographically-matched controls performed a visual selective attention task while undergoing high-density magnetoencephalography (MEG). Neuronal activity related to selective attention processing was quantified and compared across the three groups, and correlated with neuro-psychological measures of attention and executive function. Spontaneous neural activity was also extracted from these attention-related cortical areas and examined with respect to HAND status. Results: HIV-infected participants with and without HAND exhibited behavioral selective attention deficits on the MEG task, as indicated by an increased flanker effect. Neuronal measures of flanker interference activity in the alpha and theta range revealed differential dynamics in attention-related brain areas across the three groups, especially in those with HAND. In addition, theta range flanker interference activity in the left inferior frontal and dorsolateral prefrontal cortex was associated with executive function and attention composite scores, respectively. Progressively stronger spontaneous alpha and theta activity were also found in unimpaired HIV-infected and HAND participants relative to controls across brain regions implicated in different components of attention processing. Conclusions: Behavioral and neuronal metrics of selective attention performance distinguish participants with HAND from controls and unimpaired HIV-infected participants. These metrics, along with measures of local spontaneous neural activity, may hold promise as early markers of cognitive decline in HIV-infected participants and be useful prognostic indicators for HAND.