Background: Surgical ablation for atrial fibrillation (AF) is strongly recommended in patients undergoing mitral valve (MV) surgery but is underutilized. Left atrial appendage occlusion (LAAO) in patients with AF undergoing cardiac surgery is a matter of debate, and it is not clear which patients derive long-term benefit. This issue has not been investigated in United States Veterans. Methods: We performed a retrospective review of 1289 patients with pre-operative AF who underwent MV surgery between 2010–2020. Patients were grouped based on whether their procedure included ablation and LAAO, LAAO without ablation, or neither. Cox proportional hazard models, adjusted for covariates, were used to calculate risk for stroke, myocardial infarction (MI), and death based on intervention. Results: Ablation was performed in 645/1289 (50.0%) of patients and LAAO without ablation was performed in 186/1289 (14.4%) patients. Mean follow-up was 4.1 ± 3.1 years. Patients who underwent ablation had a 62% lower long-term risk of stroke (0.38, 95% CI: 0.22–0.67, p < 0.001) and 20% lower long-term mortality risk (adjusted hazard ratios (aHR) 0.80, 95% CI: 0.66–0.95, p = 0.012), but no difference in risk of MI (aHR 0.67, 95% CI: 0.38–1.16, p = 0.15). LAAO was not associated with differences in long-term risk of stroke, MI, or death. There were no differences in perioperative complications between groups. Conclusions: In veterans with AF undergoing MV surgery, ablation was inversely and independently associated with long-term stroke risk and long-term mortality, with no increased risk of perioperative complications. LAAO did not reduce long-term stroke risk.