Objective To evaluate the effect of sitagliptin on skeletal muscle expression of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1 alpha), irisin, and phosphoadenylated adenylate activated protein kinase (p-AMPK) in a rat model of type 2 diabetes mellitus (T2DM). Methods A high-fat diet/streptozotocin T2DM rat model was established. Rats were divided into T2DM, low-dose sitagliptin (ST1), high-dose sitagliptin (ST2), and normal control groups (NC). PGC-1 alpha, irisin, and p-AMPK protein levels in skeletal muscle were measured by western blot, and PCG-1 alpha and Fndc5 mRNA levels were assessed by reverse transcription-polymerase chain reaction. Results Fasting plasma glucose (FPG), fasting insulin (FIns), homeostatic model assessment-insulin resistance (HOMA-IR), and tumor necrosis factor-alpha (TNF-alpha) were significantly up-regulated in the T2DM compared with the other groups, and FPG, FIns, total cholesterol, triglycerides, TNF-alpha, and HOMA-IR were significantly down-regulated in the ST2 compared with the ST1 group. PGC-1 alpha, irisin, and p-AMPK expression levels decreased successively in the ST2, ST1, and DM groups compared with the NC, and were all significantly up-regulated in the ST2 compared with the ST1 group. Conclusion Down-regulation of PGC-1 alpha and irisin in skeletal muscle may be involved in T2DM. Sitagliptin can dose-dependently up-regulate PCG-1 alpha and irisin, potentially improving insulin resistance and glycolipid metabolism and inhibiting inflammation.