Recent studies have shown that soybean protein and its peptides have cholesterol-lowering activities. However, it is not clear whether these peptides could overcome physiological barriers, such as phase II metabolism in gastrointestinal tract and poor permeability, to reach the blood stream in its intact form. Therefore, the transepithelial transport characteristics of soybean peptide Trp-Gly-Ala-Pro-Ser-Leu (WGAPSL) with cholesterol- lowering activity were investigated in Caco-2 cells. In this study; the transepithelial absorption of WGAPSL was studied using human intestinal Caco-2 cell monolayers. The results showed that WGAPSL had good stability (83.9% ±1.98%) after simulated gastric and intestinal digestion. During the apical (AP) side to basolateral (BL) side transport, WGAPSL was absorbed intact through Caco-2 cell monolayers with apparent permeability coefficient (Papp) values of 4.4 × 10−8 to 1.2 × 10−8 cm/s. Cytochalasin D loosened the tight junctions of Caco-2 cell monolayers and significantly (p < 0.05) improved the transport process. Sodium azide, wortmannin, and Gly-Pro had minimal effects on transport, demonstrating that the major transport route of WGAPVL was paracellular via tight junctions. Finally, LC-MS analysis showed that Gly-Ala-Pro (GAP) was the important part for the intact absorption of WGAPVL and Trp (W) was the most unstable amino acid residue.