We aimed to evaluate the effect of chitosan oligosaccharide (GO2KA1) supplementation on glucose control in subjects with prediabetes. This study was a randomized, double-blind, placebo-controlled clinical trial. Subjects with prediabetes were randomly assigned to the GO2KA1 intervention group or the placebo group for 12 weeks. We assessed the serum levels of glucose, insulin, and C-peptide by a 2 hour value in the 75 g oral glucose tolerance test (OGTT), HbA1c, pro-inflammatory cytokines, and plasma adiponectin at baseline and after the 12 week intervention. The treatment group showed a significant decrease in the serum glucose level at 30 min (p = 0.013) and at 60 min (p = 0.028). The change of the serum glucose level at 60 min was significant in the treatment group compared with the placebo group (p = 0.030). Also, the plasma level of HbA1c (p = 0.023) and the pro-inflammatory cytokines (IL-6 and TNF-α) were reduced and plasma adiponectin was increased in the GO2KA1 intervention group after the 12 week treatment. However, the placebo group did not show any significant changes in these biomarkers. In subjects with prediabetes, 12 week supplement with GO2KA1 may help control postprandial glucose compared with control.