Background: Learner agency is recognised as a critical attribute in health professions education, influencing students’ motivation, engagement, and capacity for self-regulated learning. However, the relationship between assessment practices and learner agency in medical education remains underexplored. Objective: This study explored the perceptions and experiences of undergraduate medical students regarding assessment practices and their influence on the development of learner agency within the MBBS programme at IMU University. Methods: A qualitative phenomenological design using focus group discussions (FGDs) was employed to examine the experiences of 27 medical students across Years 1 to 4. A purposive sample of 21 females and 6 males from diverse backgrounds participated in seven online FGDs conducted via Microsoft Teams©. Each session included 3–5 students. Data was analysed using iterative transcript review, inductive coding, and thematic analysis. Results: Three main dimensions of learner agency—environmental, behavioural, and intrapersonal—emerged as central to students’ experiences. Continuous assessments and timely, constructive feedback supported engagement and self-regulation. However, variability in feedback quality, limited student voice in assessment design, and lack of clarity in expectations hindered students’ sense of control and ownership of learning. Conclusion: Assessment practices significantly influence the development of learner agency among medical students. Enhancing the quality of feedback, promoting opportunities for co-agency, and designing student-inclusive assessment systems may strengthen learner empowerment and self-directed learning within medical education.