Research on the impact of peer education (PE) on learning outcomes has produced inconclusive results, partly due to the methodology employed in such studies. There is a necessity to design blind, controlled studies. Further, quantitative approaches to evaluating PE may not provide a complete picture of the impact of PE on learning outcomes. The aim of the study was to determine the effect of peer education on students' academic achievement and to explain students' lived experience of participating in a PE program. The study employed an exploratory, sequential mixed-method design and occurred in two distinct and consecutive phases. The first phase consisted of a cluster-controlled, double-blind educational trial; the second, of a qualitative conventional content analysis. Data was collected during the second semester from February to July 2015 from undergraduate students. Analysis of the pre- and post-tests has been performed to evaluate the program among those enrolled in nursing and midwifery (intervention groups) and anaesthesia nursing (control group) in physiology and anatomy courses. PE resulted in significant differences in the physiology post-test scores and the anatomy post-test scores in favour of midwifery and nursing students respectively (intervention groups). Statistically significant improvement was not achieved based on formal academic exams. Themes were identified by analysing the content of qualitative feedback, with “facilitated learning” being the main theme emerging from the data. The PE program promoted learning based on the facilitator-based examination (based on post-test scores). However, PE did not improve learning in blinded condition in the current study (formal academic exam).