Although fenestration is used to improve the postoperative course of Fontan patients, the effect of fenestration on the extracardiac Fontan seems controversial especially at early postoperation. One hundred and eighty-three patients from January 2004 to June 2013 undergoing an extracardiac Fontan operation were retrospectively selected for this study. We divided the patients into low risk (93 patients) and high risk (90 patients) groups according to the risk factors recognized by previous studies and then compared the perioperative data between the nonfenestrated and fenestrated patients in each group. In both groups there was no significant difference in preoperative and operative data between the nonfenestrated and fenestrated patients. The postoperative blood oxygen saturation of fenestrated patients was significantly lower (p < 0.01) in each group. In the high risk group the chest tube volume (1153 mL vs. 1739 mL, p = 0.021) and chest tube duration (11.9 days vs. 17.0 days, p = 0.028) of fenestrated patients were lower comparing to nonfenestrated patients, while the chest tube volume and chest tube duration were similar between the nonfenestrated and fenestrated patients in the low risk group. The morbidity and mortality of nonfenestrated and fenestrated patients were similar in both groups (p > 0.05). Although fenestration was associated with lower postoperative oxygen saturation, fenestration showed better postoperative outcomes regarding the chest tube volume and duration for the high-risk patients. Considering the similar early postoperative outcomes of nonfenestrated and fenestrated patients in low risk group, our data indicate that fenestration for the high-risk patients should be performed.