Intrapulmonary-artery septoplasty may be effective for establishing two-lung Fontan circulation in patients with unilateral pulmonary circulation. However, evaluation of the function of each lung by conventional modalities can be challenging in these patients due to differing sources of blood flow to the left and right lungs following intrapulmonary-artery septation. Herein, we report a case in which two-lung Fontan circulation was successfully achieved after using cardiac MRI along with conventional modalities to evaluate pulmonary circulation.