Background Coronary artery disease (CAD) is among the main causes of hospitalization and death worldwide, therefore, the implementation of programs to reduce its impact is necessary. Supervised cardiac rehabilitation has been shown to have positive effects on CAD control. However, there are barriers to patient participation in the traditional, face-to-face cardiac rehabilitation programs, mainly in low-resource environments. Objective This study aimed to verify patient compliance to a home-based cardiac rehabilitation program, which includes unsupervised health education and physical exercises, guided by telephone. Moreover, we compare this new method to the traditional supervised cardiac rehabilitation offered in most hospital centers. Methods We present here a two-arm, single-blinded, and randomized controlled design protocol, which compares the traditional cardiac rehabilitation (CenterRehab) with the home-based cardiac rehabilitation (Home-Based) in 72 patients affected by CAD. The primary outcome is the compliance to the cardiac rehabilitation sessions. The secondary outcomes (to evaluate effectiveness) include measurable variables such as functional capacity, CAD risk factors (blood pressure, waist circumference, glycemic, cholesterol levels, depressive symptoms, and the level of physical activity), the patient’s quality of life, the disease knowledge, and the morbidity rate. Parameters such as the program cost and the usability will also be evaluated. The programs will last 12 weeks, with a total of 60 rehabilitation and 6 educational sessions. Patients of the CenterRehab program will participate in 24 supervised sessions and 36 home sessions, while the patients of the Home-Based program will participate in 2 supervised sessions and 58 home sessions, guided by telephone. After the 12-week period all participants will be recommended to continue practicing physical exercises at home or at a community center, and they will be invited for re-evaluation after 3 months. The outcomes will be evaluated at baseline, and after 3 and 6 months. Results Participants are currently being recruited for the trial. Data collection is anticipated to be completed by October 2019. Conclusions This is the first study in Brazil comparing the traditional cardiac rehabilitation approach with a novel, home-based protocol that uses an accessible and low-cost technology. If positive results are obtained, the study will contribute to establish a new and viable model of cardiac rehabilitation. Trial Registration ClinicalTrials.gov NCT03605992; https://clinicaltrials.gov/ct2/show/NCT03605992 International Registered Report Identifier (IRRID) DERR1-10.2196/13901