Executive functions are higher-order cognitive abilities that affect many of our daily actions, including reading. A two-system model for cognitive control comprises a bottom-up system composed of the dorsal and ventral attention networks and a more evolved top-down system involving the frontoparietal and cingulo-opercular networks. We examined both within- and between-network functional connectivity of these four networks in 26 8–12-year-old children with readong difficulties and 30 age-matched typical readers using resting-state functional MRI. Fluency and nonfluency behavioral reading measures were collected, and the scores were analyzed together with the functional data. Children with reading difficulties did not differ in functional connectivity for the four networks compared to typical readers. Grouping the entire cohort into low vs. high fluency-level reading groups, however, revealed significantly higher functional connectivity values within the cingulo-opercular and ventral attention cognitive-control networks for the high fluency group. Higher functional connectivity Trends between the cognitive-control networks were also observed in the high fluency group compared to the low fluency group. A similar analysis using a nonfluency word-reading task grouping did not uncover differences between the two groups. The results emphasize the complexity of the fluency task, as a test that relies on cognitive-control abilities, at both the bottom-up and top-down levels. Therefore, it may be posited that the fluency task may also be a challenge for typical readers despite their intact performance. The results reinforce the relationship between fluent reading and functional connectivity of the cognitive-control networks, emphasizing the various cognitive-control abilities that underlie this complex reading ability.