Background Obesity is among the most significant health challenges facing today’s adolescents. Weight gain during adolescence is related to cardiovascular disease, type 2 diabetes, and some cancers in later life. Presently, adolescents living in Australia have limited access to age-appropriate obesity prevention services. Objective This study aims to investigate whether a two-way text message program, with optional telephone health counseling, improves body mass index (BMI) z score and lifestyle outcomes in adolescents who are overweight. Methods This study will be a single-blind randomized controlled trial (N=150) comparing a two-way text message intervention, with optional telephone health counseling, to usual care in adolescents (13-18 years old, inclusive) who are overweight (recruited from a pediatric weight management clinic and the broader community in Sydney, Australia). The intervention group will receive a six-month text message program, which consists of two-way, semipersonalized, lifestyle-focused text messages (four messages/week) in addition to usual care. The control group will be assigned to receive usual care. The study also includes a follow-up at 12-months. The primary outcome is a change in BMI z score at six months. Secondary outcomes are changes in waist-to-height ratio, diet, physical and sedentary activity levels, sleep quality, quality of life, self-esteem, self-efficacy, social support, and eating disorder and depression symptoms. Also, we will examine acceptability, utility, and engagement with the program through a study-specific process evaluation questionnaire, semi-structured telephone interviews, and an analysis of health counselor communication logs. The analyses will be performed by the intention-to-treat principle to assess differences between intervention and control groups. Results The study opened for recruitment in December 2019. Data collection is expected to be completed by December 2021, and the results for the primary outcome are expected to be published in early 2022. Conclusions This study will test the effectiveness of an interactive two-way text message program compared to usual care in improving BMI z score and lifestyle outcomes in adolescents with overweight. This interactive, innovative, and scalable project also aims to inform future practice and community initiatives to promote obesity prevention behaviors for adolescents. Trial Registration Australia New Zealand Clinical Trials Registry (ANZCTR) ACTRN12619000389101; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=377158&isReview=true International Registered Report Identifier (IRRID) DERR1-10.2196/16481