For 44 ME/CFS and 26 HC, resting state and Stroop task fMRI were spatially normalized with a method optimized for the brainstem. After physiological signal (RETROICOR) denoising in CONN, BOLD correlations were computed between 12 brainstem reticular activation system (RAS) ROI seeds. A survey of connections showed fewer were significant in ME/CFS than HC at Rest, indicating impaired RAS function. During Task, although the same number of connections were active for the two groups, many were between different ROIs, suggesting compensatory mechanisms may be involved. Nerve signal conduction in the brainstem RAS was shown to be impaired in ME/CFS.