HighlightsThe functional architecture among regulatory structures, and the whole brain, is less modular in confirmed cases of SUDEP and those at high-risk.Altered functional organisation may mean potential impairment of communication among key regulatory circuits.SUDEP is associated with regional connectivity disruptions among cortical and sub-cortical regulatory sites.Medial thalamic connectivity was significantly altered in SUDEP compared with all control groups, including those at high-risk.Increases in the number, and a shift in organisation, of hubs appears to relate to lower mortality risk.