Nine studies met inclusion criteria: six with repeated-measures designs conducted at different times of day and three cross-sectional studies. Sample sizes ranged from 16-192 participants, mostly healthy adults in their late 20s. Across chronotypes, stronger thalamo-sensory connectivity was observed in the morning and reduced visual–motor coupling by evening (p = 0.031). Somatomotor network connectivity increased in the evening (p < 0.01), whereas ventral attention and visual networks were more dominant in the morning (p < 0.05). Evening chronotypes exhibited decreased default mode network (DMN) connectivity associated with lower attention task performance (p < 0.05), stronger precuneus–medial prefrontal cortex coupling (p = 0.002) linked to poorer sleep quality (p = 0.009) and reduced anterior cingulate cortex and insular connectivity (p < 0.05) compared to morning types. Both JBI and AXIS assessments indicated a low to moderate risk of bias across studies.