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This study explores the impact of the COVID-19 pandemic on the motivation of medical students using a mixed-method, user-led approach with students as both participants and researchers. Data were collected in 2021 through essays describing students’ motivation during the pandemic. The essays were coded, categorized, quantified, and statistically analyzed for gender-based differences. Results showed that while 71% of students reported increased motivation, female students more often experienced fluctuating motivation levels. Key motivational factors included career aspirations and educational purpose, whereas demotivational factors involved disruptions to college life and mental health struggles. Notably, female students disproportionately expressed doubts about the medical profession. The study also utilized a collaborative autoethnographic method to explore the researchers’ own pandemic experiences, revealing long-term positive effects and resonating with initial findings. This research contributes to understanding the pandemic’s long-term impact on medical students and offers insights into nurturing resilient future doctors capable of handling healthcare crises.