Background: Globally, there is an excess of 68.5 million people who have been forced to leave their homes and seek sanctuary elsewhere because of poverty, persecution, conflict, violence, and human rights violations. Although international humanitarian responses usually focus on ensuring that the basic needs of these people are being met, there is growing attention on the role that development-oriented interventions can play in the longer term. Higher education in a refugee context is one such intervention that can equip refugees with the knowledge and skills they need to serve their communities and move forward. Objective: This study aims to evaluate the outcomes and effectiveness of the University of Geneva InZone-Raft Basic Medical Training Course in the Kakuma refugee camp in Kenya compared with a previous incarnation of the same course in the Dadaab refugee camp in Kenya. Methods: We used a quasi-experimental design to compare the posttest scores of both inequivalent student groups: control group (n=18) and intervention group (n=16). Factors that influenced refugee students’ knowledge acquisition, the amount of knowledge they acquired, and their academic outcomes were assessed, and the pedagogical evolution of the project is presented. Results: We found that the Kakuma intervention course yielded better outcomes and was more effective in terms of learning than the Dadaab control course. Of the 16 students who took part in the intervention course, 10 (63%) completed the program successfully and received accreditation from the University of Geneva. We observed that they received new knowledge well and scored higher on all learning modalities than those in the control course. Comparison of written and oral examinations between the courses showed statistical significance for the intervention group in written and oral exams (two-tailed: P=.006 and P=.05; one-tailed: P=.003 and P=.03, respectively). The Kakuma course was not effective in addressing electricity and internet access problems, nor in reducing the challenge of tight deadlines in the syllabus. Pedagogical adjustments to the intervention course improved student involvement, with higher participation rates in quizzes (10/11, 91%), and overall satisfaction and learning. Conclusions: The intervention group—with an improved mode of delivery, better contextualized content, and further interaction—reached a higher level of medical knowledge acquisition and developed more complex questions on medical topics than the control group. The positive outcome of this project shows that given the right resources and support, refugees can contribute to the improvement and development of health care in their communities. Nonetheless, a more focused effort is necessary to meet the educational needs of refugee learners and better understand their living conditions.