The additive effect of high-intensity interval training to fish oil supplementation on newly diagnosed type 2 diabetes is unknown. 173 newly diagnosed type 2 diabetes patients were randomly assigned into the control group (received corn oil), fish oil group (eicosapentaenoic acid, EPA:docosahexaenoic acid, DHA = 3:2, total 2.0 g/day), and the fish oil + high-intensity interval training group. Three instructed high-intensity interval training sessions (Monday, Wednesday, and Friday; 10 x 60-s cycling bouts) were performed for 3 months. Glycaemic control was assayed by serum haemoglobin A1c, fast glucose, fast insulin, and adiponectin. Homeostatic model assessment of insulin resistance was utilized to determine the homeostasis of pancreatic function. Fat mass, triglycerides, total cholesterol, low-density lipoproteins, and high-density lipoproteins were measured to indicate cardiovascular risk. Within and between groups analysis were performed with linear mixed-effects modeling (95% Cls and p values). When compared with fish oil, fish oil + high-intensity interval training intervention has significant additive beneficial effects on haemoglobin A1c (p<0.01), fast glucose (p<0.001), homeostatic model assessment of insulin resistance (p<0.05), adiponectin (p<0.05), fat mass (p<0.01), and total cholesterol (p<0.01), but not on fast insulin level to newly diagnosed non-obese type 2 diabetes. High-intensity interval training has an additive effect on fish oil supplementation on glycaemic control, insulin resistance, cardiovascular risk, and fat mass, which indicates the potential necessity of combining high-intensity interval training with fish oil.