Background Research ethics and ethical research practice are essential for protecting research participants. However, opportunities for practical ethics learning are often limited, making it difficult to apply ethical principles in real-world research. This study explored students’ and faculty’s experiences and perspectives on ethical research conduct and learning in Rwandan medical and health sciences education. Methods An exploratory qualitative design was employed, using in-depth interviews with nineteen students and seventeen faculty staff between March and September 2024 at a medical and health sciences college of the University of Rwanda. Data were analysed and three themes were developed using reflexive thematic analysis: research ethics learning context, superficial understanding of research ethics concepts and principles, and barriers to translating knowledge of research ethics into practice. The constructivist and phenomenological frameworks were used to interpret the findings. Results While students recognized the importance of research ethics, their learning experiences were fragmented, procedural, and often burdensome. Challenges included overcrowded classes, inconsistent guidance, limited exposure to ethics materials, and lecturers’ lack of confidence in teaching ethics. Institutional inefficiencies, financial constraints, and pressures to meet academic timelines further hindered students’ preparedness for ethical research. In practice, students navigated complex situations, including populations unfamiliar with their rights, students and community expectations, and misunderstandings related to compensation for research participants, which complicated consent and blurred ethical boundaries. Conclusions The findings suggest that meaningful ethics learning occurs when ethical reasoning is embedded in day-to-day research practice and supported by mentorship, dialogue, and opportunities for real-world research engagement. Considering these results, the University of Rwanda can strengthen supervision, streamline review, ethical approval and ethical follow-up processes, and foster an environment that rewards ethical reflection. Aligning ethics education with students lived realities and experiences, and the structural constraints identified can help develop reflective, resilient practitioners equipped to navigate the complex ethical demands.