Despite the increasing incidence of acute coronary syndrome (ACS) in Japan, its prognosis has improved. However, there is a paucity of longitudinal registry data providing trends of in-hospital care and prognosis of ACS in Japan. ACS patients undergoing percutaneous coronary intervention (PCI) included in the Shinken Database 2004–2014 were divided into two groups according to admission year (2004–2009, n = 390; 2010–2014, n = 328). Patient characteristics, lesion/procedure characteristics, medications at discharge, all-cause mortality, cardiovascular death, acute myocardial infarction (AMI), target lesion revascularization (TLR), re-PCI to new lesion, and coronary artery bypass graft (CABG) within 2 years after discharge were compared between the groups. Prevalence of hypertension, dyslipidemia, and dual antiplatelet/statin prescription increased significantly between periods. Usage of second-generation drug-eluting stents (DES) increased markedly between the two periods (2.6, 66.8%), while those of bare metal stents (64.4, 26.5%) and first-generation DES (25.6, 1.5%) decreased (all, p < 0.01). Two-year event-free survival rate increased for all-cause mortality (94.6–98.3%, p = 0.01), TLR (79.4–96.1%, p < 0.01), and re-PCI to new lesion (87.3–95.1%, p < 0.01). There were no significant differences in cardiovascular death, AMI, or CABG between the two periods. The event-free rates for TLR and re-PCI to new lesion in ACS patients have increased over the last decade in Japan. These observations should be confirmed in larger, longitudinal, multicenter registries.