The objective of this study was to determine the incidence, risk factors, outcome, and clinical significance of pericardial effusion (PE). We retrospectively analyzed outcomes of 272 pediatric patients undergoing their first hematopoietic stem cell transplantation (HSCT) from 1998 to 2016. In total, 15% (3/20) and 5.9% (15/252) of autologous and allogeneic HSCT recipients, respectively, were identified with PE. However, there was no statistically significant difference in the incidence of PE between the 2 groups. The mean age at transplantation was 11.12 ± 5.41 y. Eighteen patients developed PE at 4.13 ± 4.44 mo after HSCT. PE was confirmed by echocardiogram in all patients. Three patients presented with severe PE with cardiac tamponade and required urgent pericardiocentesis. Overall survival (OS) rates for patients who developed PE were 83.3% and 38.9% at 100 d and 3 y, respectively, after HSCT. Death was not directly attributable to PE in patients who died in the first year after HSCT. Multivariable analysis identified the following variables to be associated with OS: PE (relative risk[RR]: 3.70; 95% confidence interval [95% CI]: 1.89-7.23; P < 0.001), active disease at HSCT (RR: 1.59; 95% CI: 1.02-2.49; P < 0.001), and thalassemia (RR: 0.62; 95% CI: 0.45-0.84; P < 0.001). PE is, thus, a debilitating and significant complication of pediatric HSCT. Therefore, prospective studies are required for better determination of the etiology and optimal method of PE treatment after HSCT.