Our purpose was to determine the effects of teneligliptin and sitagliptin, two dipeptidyl peptidase 4 inhibitors (DPP4-Is) with different half-lives, on glycemic variability and glucagon-like peptide-1 (GLP-1) levels in Japanese patients with type 2 diabetes mellitus (T2DM). The study subjects were 14 drug-naïve patients with T2DM who were allocated to either a 20 mg/day teneligliptin group (n = 7) or a 50 mg/day sitagliptin group (n = 7) for 7 days, then switched to the other treatment for another 7 days. Meal tolerance tests were performed at the time of no treatment, and after treatment with each DPP4-Is at supper. We evaluated the effects of each drug on glucose fluctuation using continuous glucose monitoring (CGM). There was no significant difference between the two groups in the primary endpoint (maximum glucose level after supper), nor in the secondary endpoint: area under the curve (AUC) for plasma glucose (≥140 mg/dl) after supper (18:00 - 24:00). Teneligliptin significantly improved the AUC for plasma glucose (≥140 mg/dl) after supper (20:00-24:00) (P = 0.048), and also significantly increased the GLP-1 level at 30 minutes after the meal load (P = 0.030). No serious adverse effects were noted in either group, apart from a few episodes of asymptomatic hypoglycemia. A daily dose of teneligliptin improved the AUC for plasma glucose at 20:00 to 24:00 (≥140 mg/dl) after the meal tolerance test, and also significantly increased the levels of activated GLP-1 after the test meal.