In summary, we cloned and characterized CsMRP4 using computational, molecular, and biochemical approaches in this study. In addition to structural similarities, sequence similarities were also found between CsMRP4 and human MRP4 (39% identity), and CsMRP4 was confirmed as belonging to the ABCC family. A reliable tertiary structure of CsMRP4 was also modeled and shown to have a common structural fold, MSD1-NBD1-MSD2-NBD2. When binding affinities of CsMRP4 with nine bile acids were tested through virtual docking simulation, the results indicated that CsMRP4 could be regarded as a bile transporter. The NBD2 of CsMRP4 was conserved more than NBD1, which was therefore used as a CsMRP4-specific antigen for subsequent immunohistochemistry experiments. In the metacercariae and adults of C. sinensis, CsMRP4 was found to be mainly distributed in mesenchymal tissues, which suggested that these tissues are regions of strategic importance for transporter functions throughout the fluke’s body. These findings suggest that CsMRP4 plays a role in exporting bile acids and inhibitors. The results from this study will also serve as a platform for further research on other bile transporters and homologues in flukes.