Background: Problem-Based Learning (PBL) has become a widely adopted educational strategy in medical education, emphasizing student-centered learning and the development of essential clinical competencies. However, there is ongoing debate regarding its long-term impact on graduate competencies compared to conventional lecture-based learning. This study aims to compare the long-term effects of PBL and conventional curricula on the competencies of medical graduates in clinical reasoning, communication, and teamwork. Methodology: A retrospective, comparative study was conducted at Kabir Medical College, Gandhara University, Peshawar and Nowshera Medical College, Nowshera Pakistan with 200 medical graduates - 100 from a PBL curriculum and 100 from a conventional curriculum at Competencies in clinical reasoning, communication, and teamwork were assessed using structured questionnaires, performance evaluations (Mini-CEX), and multisource feedback. Statistical analysis was performed using chi-square tests to determine the significance of competency differences between the two groups. Results: PBL graduates demonstrated significantly higher clinical reasoning (p < 0.05) and teamwork skills (p < 0.01) compared to conventional graduates. Communication skills were comparable between the two groups (p > 0.05). Overall, PBL graduates exhibited a higher percentage of high competency levels across all domains (88% vs. 75%, p < 0.05). Conclusion: The study concludes that PBL has a long-term advantage in fostering critical clinical competencies, particularly in clinical reasoning and teamwork. While communication skills did not differ significantly, PBL graduates tend to be better prepared for real-world clinical practice. These findings suggest that medical curricula should consider incorporating more PBL elements to enhance the development of well-rounded physicians.