Many factors will determine the quality of life at long-term follow-up after the Fontan operation. We tried to predict the long-term outcome of modified Fontan operation based on the combined assessment of various preoperative data. The preoperative condition was evaluated by a scoring system in which multilevel scores (from zero to 8 points) were given to a total of 14 morphological and physiological factors according to the contribution of each factor to mortality. The major factors were the association of the extracardiac total anomalous pulmonary venous connection, pulmonary arterial vascular resistance, mean pulmonary arterial pressure, PA index, ejection fraction of the main ventricle, and creatinine clearance. Points for each factor were determined according to surgical mortality, with zero points indicating no increased risk. The total score, i.e., the sum of the points for each item, in each patient was analyzed in relation to the patient's quality of life over a long-term follow-up, as evaluated by questionnaires. Twenty-six of 29 patients with scores of 5 or less showed normal or almost normal life long after the operation, whereas 5 of 10 with higher scores had restricted physical and daily activity. In conclusion, good preoperative condition predicts a good quality of life long after the Fontan operation. In addition, the concept of taking into account all possible risk factors as a comprehensive indicator may be useful in predicting long-term results.