Patients with unbalanced pulmonary artery growth resulting from pulmonary coarctation are considered unsuitable candidates for the Fontan procedure. Particularly, patients with right isomerism pose a challenge. We aimed to investigate the use of primary central pulmonary artery plasty at initial palliation in patients with right isomerism. We recruited 34 right isomerism patients with pulmonary atresia and pulmonary coarctation who underwent modified Blalock-Taussig shunt with or without primary central pulmonary artery plasty between 1998 and 2014. We classified them into the primary central pulmonary artery plasty (group P) and no primary central pulmonary artery plasty (group N) groups. We retrospectively analyzed reintervention for pulmonary artery after initial palliation, difference in size between the left and right pulmonary arteries, overall survival, success of the Fontan procedure. The group P and group N included 25 and 9 patients, respectively. Five (20%) and six (67%) patients in group P and group N, respectively, required reintervention for pulmonary artery after initial palliation (p = 0.017). No patient underwent reintervention for the pulmonary artery before bidirectional cavopulmonary shunt in group P. There was a significant difference in the bilateral pulmonary artery size balance between the groups before bidirectional cavopulmonary shunt (p = 0.041). The two-lung Fontan procedure was successful in 14 (56%) and 1 (11%) patient in group P and group N. Primary central pulmonary artery plasty may contribute toward improving the balance in the size of the PA and preclude the need for reintervention for PA.