Teen pregnancy rates in the USA remain higher than any other industrialised nation, and pregnancies among Hispanic adolescents are disproportionately high. Computer-based interventions represent a promising approach to address sexual health and contraceptive use disparities. Preliminary findings have demonstrated that the Health-E You/Salud iTu, computer application (app) is feasible to implement, acceptable to Latina adolescents and improves sexual health knowledge and interest in selecting an effective contraceptive method when used in conjunction with a healthcare visit. The app is now ready for efficacy testing. The purpose of this manuscript is to describe patient-centred approaches used both in developing and testing the Health-E You app and to present the research methods used to evaluate its effectiveness in improving intentions to use an effective method of contraception as well as actual contraceptive use.This study is designed to assess the effectiveness of a patient-centred computer-based clinic intervention, Health-E You/Salud iTu, on its ability to reduce health disparities in unintended pregnancies among Latina adolescent girls. This study uses a cluster randomised control trial design in which 18 school-based health centers from the Los Angeles Unified School District were randomly assigned, at equal chance, to either the intervention (Health-E You app) or control group. Analyses will examine differences between the control and intervention group's knowledge of and attitudes towards contraceptive use, receipt of contraception at the clinic visit and self-reported use of contraception at 3-month and 6-month follow-ups. The study began enrolling participants in August 2016, and a total of 1400 participants (700 per treatment group) are expected to be enrolled by March 2018.Ethics approval was obtained through the University of California, San Francisco Institutional Review Board. Results of this trial will be submitted for publication in peer-reviewed journals. This study is registered with the US National Institutes of Health.NCT02847858.