Objective: Placement of peritoneal drainage catheters intra-operatively has been shown to help prevent fluid overload in children recovering from surgery for two-ventricle heart disease. We aimed to determine whether this practice is also helpful in children recovering from Fontan palliation. Material and methods: A retrospective review was performed on children with single-ventricle anatomy undergoing Fontan palliation at our institution from 2007 to 2011. Variables in those with peritoneal drainage were compared with those without using t-tests, Mann–Whitney U-tests, chi-square tests, or analysis of variance for repeated measures as appropriate. Data were represented as mean with standard deviation unless otherwise noted. Results: A total of 43 children were reviewed, 21 (49%) with peritoneal drainage catheters. No complications from catheter placement occurred. The groups did not differ with regard to cardiopulmonary bypass duration, dominant ventricle, pre-operative haemodynamic data, fenestration use, and initial intensive care unit ventilation index. Central venous pressures, vasoactive medication use, and diuretic use during the first 48 hours were also not statistically different. At 48 hours, the median fluid balance was −9 (interquartile range : −50, +20) in those with peritoneal drainage and +77 cc/kg (interquartile range : +22, +96) in those without (p < 0.001), yet median duration of mechanical ventilation was 40 hours (range: 19–326) in those with peritoneal drainage and 23 hours (range: 9–92) in those without, p = 0.01. Conclusion: Patients with peritoneal drainage recovering from Fontan palliation achieved negative fluid balance as compared with those without peritoneal drainage, although this difference was associated with a longer duration of mechanical ventilation.