Background Adolescent girls with mild intellectual disabilities often face challenges in achieving independence in menstrual management, highlighting the need for structured and accessible educational interventions. This study evaluated the effectiveness of a mobile application–based education program in improving independent menstrual management skills. Methods A parallel-group randomized controlled trial was conducted with 90 adolescent girls with mild intellectual disabilities and their mothers. Participants were randomly assigned (1:1) to the intervention or control group using a computer-generated sequence. The intervention group received a mobile application–based education program (Bağımsız Yapabilirim), which included instructional videos and interactive games for up to 30 min daily, while the control group received routine care. Outcomes (hand hygiene and pad-changing skills) were assessed at baseline and at 1, 3, and 8 months using structured Performance Record Sheets. Analyses were conducted according to the intention-to-treat principle using repeated-measures ANOVA based on multiply imputed datasets. Results Baseline characteristics were comparable between groups. Intention-to-treat analyses based on multiply imputed datasets revealed significant time and group × time interaction effects for both outcomes (p < .001). Hand hygiene skills showed very large improvements (Group × Time: F(1.94, 171.02) = 49.31, p < .001, η²p = 0.359; post-intervention Cohen’s d = 2.39–3.99), maintained across all follow-up assessments. Pad-changing skills also improved significantly, with medium-to-large effect sizes over time (Group × Time: F(2.38, 206.79) = 20.34, p < .001, η²p = 0.189; post-intervention Cohen’s d = 0.75–1.39). No between-group differences were observed at baseline, whereas all follow-up assessments favored the intervention group (p ≤ .001). No adverse events were reported. Conclusion The Bağımsız Yapabilirim mobile application is an effective and accessible intervention for enhancing menstrual self-management skills in adolescent girls with mild intellectual disabilities. The improvements were sustained over 8 months, demonstrating both statistical and clinical significance, and supporting the program’s potential to promote independence and practical self-care competence in this population.