Background: The role of non-linguistic factors, such as executive functions, in the reading comprehension process has been analyzed. The present research sought to investigate the relationship between executive functions and reading comprehension. Methods: In an exploratory cross-sectional study, a group of 89 fourth-grade students were evaluated, considering a balanced number of children with and without reading comprehension difficulties. Results: The results indicate that students with reading comprehension difficulties present a lowered profile with respect to both executive functions and reading variables. The path analysis indicates the presence of differences in the variables that explain reading comprehension for both groups. While in the case of students without reading comprehension difficulties, working memory has both a direct and an indirect effect, i.e., through vocabulary, on reading comprehension; in the case of children with reading comprehension difficulties, only cognitive flexibility has a direct impact. In both cases, inhibition has an indirect impact through vocabulary. Conclusions: We reflect on the differentiated role of executive functions according to the level of development of reading skills, highlighting the possibility that some skills may act in a compensatory manner in the presence of general difficulties. The role of vocabulary in the relationship between executive skills and reading is highlighted.