Chlorogenic acid (CGA) is a naturally occurring polyphenol in the human diet and plants, exhibiting antioxidant and anti-inflammatory activities. This study was conducted to investigate the effects of CGA on intestinal development and health in weaned pigs. Twenty-four weaned pigs were randomly assigned to two treatments and fed with a basal diet or a basal diet supplemented with 1000 mg/kg CGA. After a 14 d trial, samples were collected. Compared with the control group, CGA supplementation decreased the serum tumor necrosis factor-α, interleukin-6, and interleukin-1βIL-6 concentrations and elevated the serum immunoglobulin G and jejunal secretory immunoglobulin A concentrations. Meanwhile, jejunal villus height, duodenal and jejunal villus width, and jejunal and ileal villus height/crypt depth were increased by CGA. CGA not only decreased the number of duodenal and jejunal cells in the G0G1 phase but also increased the number of jejunal and ileal cells in the S phase. The percentages of late and total apoptotic cells in jejunum and the ratio of B-cell lymphoma-2-assiciated X protein to B-cell lymphoma-2 (Bcl-2) in duodenum and jejunum were also decreased by CGA supplementation. Finally, CGA upregulated the expression level of Bcl-2 in duodenum and jejunum, whereas it downregulated the expression levels of caspase-3 in duodenum and jejunum, caspase-9 in jejunum, as well as Fas in jejunum and ileum. This study suggested that the beneficial effects of CGA on intestinal development and health are partially due to improvement in immune defense and suppression in excessive apoptosis of intestinal epithelial cells in weaned pigs.