Gardenia jasminoides J.Ellis, a well-known traditional Chinese medicine, has been widely used in Asian countries for centuries. This study presented the skin barrier repair efficacy and safety evaluation of an extract from G. jasminoides. The results showed that GarPepair was primarily composed of geniposide and genipin-1-β-D-gentiobioside with concentrations of 3.39 and 1.03 mg/mL, respectively. GarPepair (1.25%, w/w), geniposide (50 μg/mL), and genipin-1-β-D-gentiobioside (50 μg/mL) showed no cytotoxicity but could significantly up-regulate mRNA level (82.5%, 54.4%, and 99.4%, respectively) and protein expression (68.7%, 57.1%, and 92.6%, respectively) of ZO-1 in HaCat cells induced by lipopolysaccharide. Moreover, GarPepair showed low acute toxicity on zebrafish with an IC50 value of 5.91% (w/w), indicating that GarPepair had high safety. In summary, we can conclude that GarPepair and its active ingredients (geniposide and genipin-1-β-D-gentiobioside) had significant skin barrier repair efficacy with high safety, making it suitable for use as an active substance in cosmetics.