Intra-individual variability of processing speed (IIV-PS) is a more sensitive discriminator between controls and MS patients in early disease stage than the normative mean scores of PS. We used rsfMRI to interrogate the neural correlates of IIV-PS and means of PS in MS patients with young-adult onset. Significant correlation of the amplitude of low-frequency fluctuations (ALFF) was found with IIV-PS but not with mean PS. Seed-to-voxel functional connectivity analysis showed significant connections associated with altered IIV of identification task, but not the IIV of detection task. This approach identified the neural networks associated with altered IIV-PS in MS.