Background: Clinical and health systems research are essential for advancing global healthcare. Engaging and training medical students in research will foster lifelong evidence-based practice, particularly for the emerging healthcare workforce. This study investigates the involvement of Nigerian medical students in research, identifying key opportunities and barriers to enhance their engagement. Methods: This cross-sectional, descriptive study used an online survey targeting recent graduates from 42 accredited Nigerian medical schools. A purposive sampling approach selected one federal, state, and private institution from each of Nigeria�s six geopolitical zones. Data were collected between February and June 2024 using a face-validated online questionnaire, which gathered quantitative data and free-text recommendations. The survey was distributed through WhatsApp groups. Descriptive statistics and thematic analysis were employed to explore trends in the data. Ethical approval was obtained from the Jos University Teaching Hospital ethics review board (JUTH/DCS/IREC/127/XXXI/871). Informed consent was secured from each participant prior to participation. Results: Of the 429 respondents (270 men, 159 women) from 15 universities across all six zones, 92 participated in research during medical school. Men engaged in more research projects than women (p = 0.03). Most respondents participated in two projects, usually group-based, with limited individual projects. Few had presented (20) or published (17) their research. Proficiency was highest in developing appropriate research methodologies (54), while data analysis was the most challenging aspect of research (42). Participation in research was supported by adequate mentorship for most participants (64), whereas time constraints(74), lack of research funding (55), and inadequate research training (31) were the main barriers to involvement. Regional differences were noted, with the highest participation by students in the South-South geo-political zone (98) and the lowest in the South-West (85). Learners from the South-West had more opportunities to present research at conferences, while those from the South-East had the fewest. Participants advocated for integrating more research opportunities into the medical curriculum, emphasising early skill development, expanding mentorship and networking opportunities, and offering grants to support students in conducting innovative research. Conclusion: There is a pressing need to enhance structured research opportunities in Nigerian medical education, especially for female medical students. This includes expanding access to training in data analysis, increasing publication and presentation opportunities, and integrating research skills early in the curriculum while addressing barriers like time constraints. Clinical trial number: Not applicable. © 2025 Elsevier B.V., All rights reserved.