Collagen-derived small peptides, such as Gly-Pro-Hyp (GPH) and Pro-Hyp (PH), play a role in various physiological functions. Although collagen degrades in the gastrointestinal tract randomly and easily, it is not readily cleaved into bioactive peptides. To increase the bioavailability of bioactive peptides, a collagen tripeptide (CTP) was prepared from fish scales by the digestion method using collagenase from nonpathogenic Bacillus bacteria. It was demonstrated that Hyp-containing peptides-GPH and PH-were better absorbed and reached higher plasma levels after the oral administration of CTPs in rats compared to high molecular weight collagen peptide (H-CP). GPH and PH were stable in gastrointestinal fluid and rat plasma for 2 h, and GPH was able to be transported across the intestinal cell monolayer. These results suggest that the ingestion of CTP is an efficient method for taking bioactive peptides orally due to the enzymatic stability and intestinal permeability of GPH and PH.