The gut-brain axis is widely influenced by the intestinal microbiota and dysbiosis is consequently associated with a large dysregulation of its functions. Probiotic supplementation, reducing the harmful effects of dysbiosis, has shown positive effects not only on gut and brain functions, but also on the control of the dangerous effects of immune activation. Mounting evidence has shown that neurocognitive impairment can be a secondary to the impairment of the microbiota-gut-brain axis in HIV positive patients. In this case report we analyzed the improvement of neurocognitive performances associated with a reduction of levels of peripheral immune-activation, after 6 months of probiotic supplementation. In this case, the achieved result may have been influenced by a more comprehensive modification of the patient’s lifestyle with the introduction of a controlled diet and regular physical activity. Our observations suggest that integrate antiretroviral therapy and non-pharmacological tools into an overall approach, can be a useful strategy to control some non-AIDS related diseases.