Objective: The preservation of pancreatic β-cell mass is an essential factor in the onset and development of type 2 diabetes mellitus. Recently, sodium- glucose co-transporter 2 inhibitors have been launched as anti-hyperglycemic agents, and their organ protective effects are attracting attention. They are also reported to have favorable effects on the preservation of pancreatic β-cell mass, but the appropriate timing for the administration of sodium-glucose co-transporter 2 inhibitors is obscure. Methods: In this study, we administered a sodium-glucose co-transporter 2 inhibitor, dapagliflozin, to an animal model of type 2 diabetes mellitus, db/db mice, and investigated the adequate timing and duration for its administration. We also conducted microarray analysis and methylated DNA immunoprecipitation (MeDIP) using pancreatic islets from db/db mice. Results: We found that dapagliflozin preserved pancreatic β-cell mass depending on the duration of administration, and markedly improved blood glucose levels. If the duration was the same, the earlier administration of dapagliflozin was more effective in preserving pancreatic β-cell mass, increasing serum insulin levels, and improving blood glucose levels. From the analysis of microarray, we discovered that the expression of Agr2, Tff2, and Gkn3 was significantly upregulated following the early administration of dapagliflozin. This upregulated gene expression might provide a legacy effect for the preservation of pancreatic β-cell mass. In addition, MeDIP analysis revealed that early administration of dapagliflozin affected DNA methylation in pancreatic islets of db/db mice. Conclusion: We expect that the early administration of dapagliflozin would provide a long-lasting effect in preserving pancreatic β-cell mass.