Resting‐state functional magnetic resonance imaging (rs‐fMRI) has the potential to shed light on the pathophysiological mechanisms of Huntington's disease (HD), paving the way to new therapeutic interventions. A systematic literature review was conducted in three online databases according to PRISMA guidelines, using keywords for HD, functional connectivity, and rs‐fMRI. We included studies investigating connectivity in presymptomatic (pre‐HD) and manifest HD gene carriers compared to healthy controls, implementing seed‐based connectivity, independent component analysis, regional property, and graph analysis approaches. Visual network showed reduced connectivity in manifest HD, while network/areas underpinning motor functions were consistently altered in both manifest HD and pre‐HD, showing disease stage‐dependent changes. Cognitive networks underlying executive and attentional functions showed divergent anterior–posterior alterations, possibly reflecting compensatory mechanisms. The involvement of these networks in pre‐HD is still unclear. In conclusion, aberrant connectivity of the sensory‐motor network is observed in the early stage of HD while, as pathology spreads, other networks might be affected, such as the visual and executive/attentional networks. Moreover, sensory‐motor and executive networks exhibit hyper‐ and hypo‐connectivity patterns following different spatiotemporal trajectories. These findings could potentially help to implement future huntingtin‐lowering interventions.