D-allulose is a rare sugar with an almost zero calorie and is known to suppress postprandial hyperglycemia and fat mass accumulation. Although D-allulose has been reported to be safe in healthy subjects and overweight/obese adults, its safety in borderline diabetes and diabetes patients has not been evaluated. Therefore, we conducted an open trial aimed to investigate the long-term safety of D-allulose in borderline diabetes and type 2 diabetes. Subjects took 5 g of D-allulose with meals three times daily for 12 continuous weeks. The general blood biochemical parameters, hematological parameters, urinary parameters, and anthropometric indicators were measured at 0, 2, 4, 8, and 12 weeks of the consumption periods and 4 weeks after completing consumption. Adverse events were assessed by the principal physician on each examination day. A total of 12 and 6 subjects with borderline and type 2 diabetes, respectively, were analyzed. No serious clinical problems were found in this study, although significant cholesterol variations and the improvements of some indicators of hepatic function were observed. In conclusion, the long-term ingestion of D-allulose is safe in borderline diabetes and type 2 diabetes. D-allulose can potentially suppress postprandial hyperglycemia and fat mass accumulation, and thus might be useful in diabetes.