The protective role of Prdx6 on rat corneal tissue against ultraviolet B injury in vivo has been confirmed previously. We further investigated the function and molecular mechanism of Prdx6 in human corneal epithelial cells under ultraviolet B radiation. The experimental groups were designed as follows: (1) Prdx6 RNAi, (2) Prdx6 RNAi + ultraviolet B radiation, (3) normal human corneal epithelial cells, (4) normal human corneal epithelial cells + ultraviolet B radiation, (5) wild-type Prdx6 overexpression, (6) wild-type Prdx6 overexpression + ultraviolet B radiation, (7) mutant-type Prdx6 overexpression, and (8) mutant-type Prdx6 overexpression + ultraviolet B radiation. The cell survival rate was detected by a Thiazolyl Blue Tetrazolium Bromide assay. Apoptosis, reactive oxygen species, and malondialdehyde were detected with a commercial kit. Gene expression was detected by real-time polymerase chain reaction. We found the following results. (1) Compared to normal cells, the survival rates were 32%, 87%, and 58% under ultraviolet B radiation in the Prdx6 interference, wild-type overexpression, and mutant-type overexpression groups, respectively. The survival rates were decreased to 50% at 24 h and 31% at 48 h when the phospholipase A2 activity of Prdx6 was inhibited after ultraviolet B radiation. (2) Apoptosis, reactive oxygen species content, and malondialdehyde levels were increased when Prdx6 was downregulated. This phenomenon became more severe under ultraviolet B radiation. (3) The expression levels of apoptosis-related and antioxidant genes all changed along with the changes in expression of Prdx6. (1) Both peroxidase and phospholipase A2 activities of Prdx6 are crucial for its protective role in corneal tissue. (2) Downregulated expression of Prdx6 resulted in high endoplasmic reticulum stress. (3) Apoptosis in human corneal epithelial cells with downregulated Prdx6 coupled with ultraviolet B radiation was related to the pathways of DNA damage and the death receptor. (4) Low levels of antioxidants are sufficient for maintaining homeostasis in human corneal epithelial cells without external stimuli. Under the condition that Prdx6 was downregulated, human corneal epithelial cells were more sensitive to ultraviolet B radiation.