Insulin resistance is associated with a poor prognosis in non‑alcoholic fatty liver disease (NAFLD) patients. Isomaltulose, a naturally‑occurring disaccharide, is reported to improve glucose and lipid metabolisms in obese patients. The present study aimed to investigate the effects of isomaltulose on insulin resistance and various metabolites in NAFLD patients. Five male patients with NAFLD consumed 20 g isomaltulose or sucrose (control). Changes in insulin resistance and metabolites were evaluated by alterations of serum C‑peptide immunoreactivity (CPR) and metabolomic analysis from baseline to 15 min after the administration, respectively. There was no significant difference in changes of blood glucose level; however, the CPR level was significantly decreased in the Isomaltulose group compared to the control group (0.94±0.89 vs. ‑0.12±0.31, P=0.0216). In a metabolomic analysis, a significant alteration was seen in 52 metabolites between the control and Isomaltulose groups. In particular, the taurodeoxycholic acid level significantly increased approximately 12.5‑fold, and the arachidonic acid level significantly decreased approximately 0.01‑fold. Together, it present study demonstrated that isomaltulose improved insulin resistance in NAFLD patients. It was also revealed that isomaltulose affects taurodeoxycholic acid and arachidonic acid. Thus, isomaltulose may have a beneficial effect on insulin resistance through alterations of bile acid and fatty acid metabolisms in NAFLD patients.