To evaluate the effectiveness of Health-E You/Salud iTu, a mobile health application (app), on increasing knowledge, self-efficacy and contraception use among Latina adolescents, its impact on visit quality, and app satisfaction. This study used cluster-randomized controlled trial (CRCT) of 18 school-based health centers (SBHCs). Prior to the visit, intervention participants received the patient-centered contraceptive decision-making support app and controls answered sexual health questions on iPads. Participants completed a previsit questionnaire and 3 follow-up surveys (48 hours, 3-, and 6-months) after the recruitment visit (where intervention participants completed the app). Differences in adolescents’ contraceptive knowledge, self-efficacy, and use over the 6-month follow-up were assessed by generalized mixed effects regression models. A total of 1,360 Latina adolescents participated; 57.2% responded to the 48-hour survey, 50.1% to the 3-month, 49.7% to the 6-month, and 42.3% to both the 3- and 6-month surveys. Health-E You users’ demonstrated significant increases in pre-post knowledge (p < 0.001). Intervention participants who completed the follow-up survey reported greater increases in mean self-efficacy from baseline (23.2 intervention vs. 22.5 controls) to 6 months (26.1 vs. 23.4; b = 1.58, 95% CI 0.38–2.77, p = 0.01), and greater increases in non-barrier contraceptive use from baseline (29% intervention vs. 30% controls) to 3 months (63% vs. 45%; OR = 3.29, 95% CI 1.04–10.36, p = 0.04) and 6 months (63% vs. 44%; OR = 5.54, 95% CI 1.70–18.06, p = 0.005). Providers and adolescents reported high app satisfaction and stated it improved visit quality. While data suggest that Health-E You improved outcomes, findings must be interpreted cautiously. Intervention participants had higher baseline sexual activity rates, more recruitment visits for pregnancy testing, emergency contraception or birth control, and lower completion rates of follow-up surveys than controls. Despite declines in adolescent pregnancy in the United States, Latinas continue to have disproportionately high rates compared to white females. The Health-E You app may be an effective support tool for both adolescents and providers in SBHCs, and possibly other clinical settings, across the country to increase contraceptive use and thereby decrease unintended pregnancies. It could potentially reduce disparities in adolescent pregnancies and create more efficient visit time spent between clients and their providers.