Background: Internet documents are characterised by their non-linear hyperlink structure, which allows for more flexible reading, at the cost of higher cognitive loads. Linear text reading comprehension skills contribute to hypertext comprehension (either directly or through its impact on navigation behaviours) but cannot fully account for its complexity. There is also evidence that hypertext reading engages executive functions, but few studies have addressed the core executive function processes simultaneously. This study examined hypertext comprehension and navigation skills and their association with linear text reading comprehension and executive functions in adolescents. Methods: One hundred thirty-six third-year students (61% boys; age: M = 14.03, SD = 0.44 years) participated in the study. Students were assessed with a paper-and-pencil expository text comprehension test, a computerised neuropsychological battery to measure executive functioning (perceptual and response inhibition, shifting and working memory [WM]) and a hypertext comprehension task. Results: We found direct contributions of shifting, linear text comprehension and navigation efficiency to hypertext comprehension. Linear text comprehension was associated with shifting, while navigation efficiency increased with WM and linear text comprehension skills. In addition, navigation partially mediated the effects of linear text comprehension and fully mediated those of WM on hypertext comprehension. Conclusions: We found direct and indirect contributions of executive function to hypertext comprehension, mediated by linear text comprehension and navigation efficiency. This suggests that finding and integrating information from hypertexts engages shifting beyond its contribution to linear text reading. The role of WM was explained by its contribution to navigation efficiency (providing a workspace to keep track of navigation paths, reading goals and inferential processing). These findings underline the relevance of high-level cognitive abilities for Internet reading in adolescents, as well as the importance of teaching boosting navigation strategies in middle school, given their impact on hypertext comprehension.