Fluent reading in children relies on executive functions (EF). Recent research suggests that EF skills also affect arithmetic abilities. Children with reading difficulties (RD) experience deficits in EF. It is still unknown to what extent these EF deficits are the basis for both reading and arithmetic skills in children with RD compared to typical readers. To define the role of EF in reading and arithmetic in children with RD and typical readers, EF measures and reading and arithmetic fluency and non-fluency measures were assessed in 8–12-year-old children with RD and age-matched typical readers. Comparison and correlation analyses were performed within and between the two groups. Children with RD scored lower on reading and arithmetic fluency and non-fluency tasks compared to typical readers. For both groups, fluency measures were lower than non-fluency measures. Strong correlations were found within the entire study population between fluency measures and EF, as well as between non-fluency measures and EF compared to mixed correlations observed for the groups separately. Fluency was related to subcomponents of EF expressed in both reading and arithmetic domains for the two groups. The role of each domain and comparison with non-fluency results for each group are discussed.