Corneal epithelial barrier dysfunction is harmful to corneal health; the pathogenesis is unclear. This study aims to elucidate the mechanism by which tryptase compromises corneal epithelial barrier function. Human corneal epithelial cell line (HCE cells) was cultured into monolayers using as a study platform. Quantitative reverse transcription polymerase chain reaction and Western blotting were employed to detect the expression of matrix metalloprotenases (MMP)9. The endosome/lysosome fusion was observed by confocal microscopy. The corneal epithelial barrier function was assessed in Transwell system. The results showed that HCE cells expressed proteinase‐activated receptor (PAR)2. Activation of PAR2 by tryptase induced expression of MMP9 in HCE cells, interfered with the fusion of endosome/lysosome, and compromised the epithelial barrier function, which could be prevented by pretreatment with MMP9 inhibitor. We conclude that tryptase can increase the expression of MMP9 in HCE cells and compromise the epithelial barrier function. Copyright © 2013 John Wiley & Sons, Ltd.