To enhance cyclo-His-Pro (CHP) content, soybean hydrolysate was obtained using the strains isolated from Chungkukjang and further purified by various purification steps. First, twenty two strains were screened from Chungkukjang containing high level of CHP. Among them, the strain No. 12, which showed higher productivity of CHP from soybean ferment and have homologous sequence with 16S rDNA of Bacillus amyloliquefaciens, was named B. amyloliquefaciens CHP-12. Through various purification processes, CHP was concentrated from soybean ferment using ultrafiltration, which showed the best efficiency of CHP production, with the yield (71.3%) and CHP content (2.14 mg/g). Moreover, when glucose tolerance test was performed in Type I Sprague-Dawley rat induced by streptozotocin using the soybean ferments [0.5 g soybean ferment/kg body weight (CHP-0.5 group)] and 1.0 g soybean ferment/kg body weight (CHP-1.0 group), there were significant differences in glucose levels between diabetes-control group (265.3 mg/dL) and soybean ferment-treated groups (CHP-0.5 group: 84.3 mg/dL and CHP-1.0 group: 85.3 mg/dL) 120 min after glucose injection (2 g/kg body weight) (p < 0.05). Accordingly, it is suggested that the soybean ferment containing high level of CHP might be a candidate material as an anti-diabetic supplement for manufacturing functional healthy foods.