Adolescents with moyamoya disease can experience unexpected transient ischemic attacks, significantly impacting their daily lives. This study aimed to examine the effectiveness of the Moyamoya Healthy Youth application for adolescents with moyamoya disease. The research employed a parallel, two‐group randomized controlled trial with a repeated measures design. A total of 64 adolescents with moyamoya disease were participated. The intervention group applied the application, whereas the wait‐list group received their usual care from an outpatient clinic. The outcome variables were assessed three times during the study, from July 2021 to March 2022. Repeated measures ANOVA and Friedman test were used to analyze results. The intervention group exhibited significant improvements in stress and health behavior. No statistically significant improvement was observed in moyamoya disease knowledge, social support, sense of coherence, depression, cortisol, and symptoms. This mobile‐based strategy empowered adolescents to monitor their health behaviors and cope with stress. This intervention is a promising strategy for health care providers to enhance self‐management skills and achieve better quality of life in such adolescents.Trial Registration: Korea Clinical Trial Registry KCT0006451. https://cris.nih.go.kr/cris/search/detailSearch.do/21925