Children in primary school read hypertext for comprehension. However, children typically are taught reading strategies for linear text, while these strategies are not automatically transferrable one-to-one to hypertext. In the present study, a training group of 55 sixth-graders were taught four hypertext reading strategies (planning, monitoring, evaluation and elaboration) via mind mapping and the usage of a prompting paper-card. A control group of 29 children received no strategy training. This study examined to what extent strategy training influenced children’s strategy use and learning outcomes: (1) number of pages read and reading time per text, (2) literal/inferential reading comprehension scores and (3) knowledge representations (relatedness judgment task and mind maps). At posttest, the training group showed higher scores on a self-reported strategy usage questionnaire, and higher comprehension scores as compared to the control group. Hypertext strategy training in combination with mind-mapping supports children’s hypertext comprehension.