Purpose The objectives of this study were to determine if HIV-infected patients treated with highly active antiretroviral therapy (HAART), without dementia, suffer from longitudinal gray matter (GM) volume loss, changes in white matter (WM) integrity and deterioration in functional connectivity at rest, in an average interval of 30 months. Methods Clinically stable HIV-positive patients (on HAART, CD4 + T lymphocyte > 200 cells/μl, and viral loads <50 copies/μl) were recruited. None of them had HIV-associated dementia. Each patient underwent two scans, performed in a 1.5-T magnetic resonance imaging (MRI) scanner. FreeSurfer was used to perform cortical volumetric reconstruction and segmentation of GM structures. WM integrity was assessed using tract-based spatial statistics to post-process diffusion tensor imaging data, and FMRIB's Software Library tools were used to post-process resting-state functional magnetic resonance imaging (RS-fMRI). Results There were no significant differences in cortical thickness, deep GM volumes, or diffusivity parameters between the scans at the two time points. Five resting-state networks were identified in our patients. In the second MRI, HIV-positive patients presented increased areas of functional connectivity in visual pathways, frontoparietal and cerebellar networks, compared with the first MRI (considering p < 0.05). Conclusions RS-fMRI revealed potentially compensatory longitudinal alterations in the brains of HIV-positive patients, attempting to compensate for brain damage related to the infection.