In Taiwan, growing vegetables often suffer from waterlogged caused by monsoon rain or cloudbursts during spring and summer. In this study, the plant growth, oxidative stress levels, and the free radical scavenging system of waterlogged sweet pepper 'Trim Star' seedlings with or without calcium chloride (CaCl2) pre-treatment were investigated. CaCl2 solutions were applied to the growing medium for 3 times at 7-day intervals beginning at the time when each seedling had 3 true leaves. Then the seedlings were subject to waterlogged for 7 days followed by 12 days of recovering growth under normal conditions before final evaluation. CaCl2 application increased the growth in size and biomass, decreased the electrolyte leakage, decreased contents of malonaldehyde, superoxide anion, and hydrogen peroxide, and promoted the activities of superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase of the waterlogged seedlings. Application of 75 mM CaCl2 significantly alleviated the damage of waterlogged in sweet pepper seedlings.