Active learning strategies are widely studied, but perspective on their effectiveness in complete undergraduate studies or about their contribution to closing the gender gap are still required. Challenge-based learning has been around for more than a decade. However, results have been collected in limited time and application environments, for example, one semester or one activity in a course. In this work, we present a quantitative study that was applied to results of the National Center for the Evaluation of Higher Education’s Engineering Bachelor’s Degree Standardized General Examination of 4226 students comparing those who received a traditional educational model and those who received a challenge-based learning educational model. A statistical analysis of communication and disciplinary competencies found that the traditional educational model induces a greater marginal significant result in the test. Additionally, we found that female students perform better in communication competencies while male students perform better in disciplinary competencies. Our results confirm that challenge-based learning is as effective as a traditional educational model when applied during complete undergraduate studies while developing competencies like critical thinking, long-term retention, leadership, multidisciplinary teamwork, and decision-making. Challenge based learning is a prolific learning strategy for evolving into a new way of teaching in undergraduate programs.