Objective To compare long-term outcomes following mitral valvuloplasty (MVP) and mitral valve replacement (MVR) for native valve endocarditis (NVE). Methods Between November 1993 and August 2016, consecutive 101 patients with NVE underwent mitral surgery in our department, MVP for 52 patients and MVR for 49 patients. There were 69 males and 32 females at age of 38.1±14.9 years. The mean follow-up was 99.4±75.8 months. Results There was no statistical difference in cardiopulmonary bypass time, aortic cross-clamp time, in-hospital mortality, duration of mechanical ventilation, ICU stay or hospital stay after surgery between the two groups. Survival rate at 1, 5, 10, 20 years after surgery was 100.0%, 97.6%, 97.6%, 97.6% for MVP, and 93.5%, 84.3%, 84.3%, 66.2% for MVR with a statistical difference between the two groups (P=0.018). There was no stroke in the patients with MVP during follow-up periods. However, stroke-free survival rate at 1, 5, 10, 20 years after surgery was 100.0%, 93.9%, 89.4%, 70.2% for MVR patients with a statistical difference between the two groups (P=0.023). There was no statistical difference in recurrence of infection, perivalvular leakage and reoperation between the two groups. Composite endpoint-free survival rate at 1, 5, 10, 20 years after surgery was 100.0%, 97.6%, 92.9%, 92.9% for MVP, and 91.3%, 79.6%, 75.8%, 51.0% for MVR with a statistical difference (P=0.006). Conclusion MVP is associated with better outcomes than MVR in the patients with NVE; generalizing MVP technique in the patients with NVE is needed.