Hospital-acquired functional decline is an important outcome that affects the long-term prognosis of patients after cardiac surgery. Phase II cardiac rehabilitation (CR) for outpatients is expected to improve prognosis; however, this is not clear in patients with hospital-acquired functional decline after cardiac surgery. Therefore, this study evaluated whether phase II CR improved the long-term prognosis of patients with hospital-acquired functional decline after cardiac surgery. This single-center, retrospective observational study included 2371 patients who required cardiac surgery. Hospital-acquired functional decline occurred in 377 patients (15.9%) after cardiac surgery. The mean follow-up period was 1219 ± 682 days in all patients, and there were 221 (9.3%) cases with major adverse cardiovascular events (MACE) after discharge during the follow-up period. The Kaplan–Meier survival curves indicated that hospital-acquired functional decline and non-phase II CR was associated with a higher incidence of MACE than other groups (log-rank,p< 0.001), additionally exhibiting prognosticating MACE in multivariate Cox regression analysis (HR, 1.59; 95% CI, 1.01–2.50;p= 0.047). Hospital-acquired functional decline after cardiac surgery and non-phase II CR were risk factors for MACE. The participation in phase II CR in patients with hospital-acquired functional decline after cardiac surgery could reduce the risk of MACE.