There have been no reports regarding the influence of a change in the pulmonary artery index before or after a Fontan operation. Moreover, the factors that might affect the change in the pulmonary artery index are unclear. This was a retrospective study, which included 94 patients who underwent a Fontan operation. We divided the patients into two groups according to the change in the pulmonary artery index before and after the Fontan operation: the increased pulmonary artery index group (n = 51) and decreased pulmonary artery index group (n = 43). The pulmonary artery index after the Fontan operation was significantly higher in the increased pulmonary artery index group than decreased pulmonary artery index group (p < 0.0001). The central venous pressure (p < 0.0001) and pulmonary vascular resistance (p = 0.007) were significantly lower in the increased pulmonary artery index group. The mixed venous oxygen saturation was significantly higher in the increased pulmonary artery index group (p < 0.0001). The pulmonary artery index was more increased in the patients who were administered a phosphodiesterase type 5 inhibitor than in those who were not (p = 0.03). The change in the pulmonary artery index reflected the hemodynamics after a Fontan operation during the short term. In that respect, phosphodiesterase type 5 inhibitors might be involved in the process.