Objective This retrospective study analyzed the outcomes of mitral valve surgery in atrial functional mitral regurgitation (AFMR) compared with those in degenerative mitral regurgitation (DMR). Methods Patients with AFMR or DMR who underwent mitral valve repair/replacement at two institutions (January 2012–December 2022) were included. We excluded patients <18 years of age, undergoing concomitant cardiac surgery except for the maze procedure or tricuspid annuloplasty. We used propensity score analysis to adjust for baseline differences. Results 642 patients were enrolled. After propensity score analysis, 164 patients were classified into the DMR and 82 patients into the AFMR. All matched patients in both groups had atrial fibrillation. In DMR and AFMR, the 5-year freedom from readmission for heart failure and cardiac death was 96.3% vs. 88.6% (p = 0.045) and 100% vs. 90.0% (p = 0.002), respectively. The recurrence ratio of significant MR after mitral valve repair was not significantly different between the two groups (Log-rank = 0.699), and the 5-year freedom from MR recurrence (≥moderate) was 89.8% and 93.0%, respectively. After the maze procedure, significantly more patients in the AFMR were in junctional rhythm than in the DMR (49.1% vs. 3.3%) (p < 0.001), needing significantly more permanent pacemaker insertion during the follow-up period (11.4% vs. 1.5%, after 5 years) (Log-rank = 0.041). Conclusions AFMR showed acceptable outcomes of mitral valve surgery, and mitral valve repair is a good treatment option. However, significantly more patients were in junctional rhythm after the maze procedure, needing more permanent pacemaker insertion.