Action videogames have been shown to induce modifications in perceptual and cognitive systems, as well as in brain structure and function. Nevertheless, whether such changes are correlated with brain functional connectivity modifications outlasting the training period is not known. Functional magnetic resonance imaging (fMRI) was used in order to quantify acute and long-lasting connectivity changes following a sustained gaming experience on a first-person shooter (FPS) game. Thirty-five healthy participants were assigned to either a gaming or a control group prior to the acquisition of resting state fMRI data and a comprehensive cognitive assessment at baseline (T0), post-gaming (T1) and at a 3 months’ follow-up (T2). Seed-based resting-state functional connectivity (rs-FC) analysis revealed a significant greater connectivity between left thalamus and left parahippocampal gyrus in the gamer group, both at T1 and at T2. Furthermore, a positive increase in the rs-FC between the cerebellum, Heschl’s gyrus and the middle frontal gyrus paralleled improvements of in-gaming performance. In addition, baseline rs-FC of left supramarginal gyrus, left middle frontal gyrus and right cerebellum were associated with individual changes in videogame performance. Finally, enhancement of perceptual and attentional measures was observed at both T1 and T2, which correlated with a pattern of rs-FC changes in bilateral occipito-temporal regions belonging to the visual and attention fMRI networks. The present findings increase knowledge on functional connectivity changes induced by action videogames, pointing to a greater and long-lasting synchronization between brain regions associated with spatial orientation, visual discrimination and motor learning even after a relatively short multi-day gaming exposure.