Visual backward masking paradigm (VB) distinguishes between conscious and unconscious processes and evaluates fundamental brain functions and cognition. Delayed consciousness was shown as related with white matter damage in early Multiple Sclerosis (MS). However, it is unknown, if regional brain activity and structural connectivity are related to delayed consciousness in MS. We investigated the impaired access to consciousness in MS[25(MS)/37(controls)] using task-based-fMRI based on the VB and its relation with structural connectivity. Lower activation was detected in unconscious-processing in MS vs controls. Strong relationship between VB-performance and lower structural connectivity in ventral-attention/visual/default-mode networks supports the sensitivity of VB in MS.