In this work we examined functional connectivity (FC) changes within and between the resting state networks (RSNs) caused by Relapsing Remitting Multiple Sclerosis (RRMS) in two cohorts showing mild disability but different disease duration. Our results demonstrate widespread functional alterations in both short and long duration RRMS groups (MS1 and MS2). The MS1 group showed more severe FC alterations compared to the MS2 group. Overall, these results suggest that there may be pathophysiological differences in RRMS groups with different disease durations. Longitudinal studies would be needed to investigate whether FC findings are able to predict the future course.