The objective of this study was to compare the hemodynamic performances and gaseous microemboli (GME) handling ability of two pediatric oxygenators in a simulated pediatric cardiopulmonary bypass (CPB) model and the importance of adding an arterial filter in the circuit. The circuit consisted of a Braile Infant oxygenator or a Maquet Quadrox‐I Pediatric oxygenator without integrated arterial filter (parallel arrangement), 1/4 in. ID tubing A‐V loop, and a 12‐Fr arterial cannula, primed with lactated Ringer’s solution and packed red blood cells. Trials were conducted at flow rates ranging from 500 to 2000 mL/min (500 mL/min increment) at 35°C and 28°C. Real‐time pressure and flow data were recorded using a custom‐based data acquisition system. For GME testing, 5 cc of air was manually injected into the venous line. GME were recorded using the Emboli Detection and Classification Quantifier (EDAC) System. An additional experiment using a separate arterial filter was conducted. There was no difference in the mean circuit pressure, pressure drop, total hemodynamic energy level, and energy loss between the two oxygenators. The venous line pressures were higher in the Braile than in the Quadrox group during all trials (P <0.01). GME count and volume at pre‐/post oxygenator and pre‐cannula sites in the Quadrox were lower than the Braile group at high flow rates (P < 0.05). In the additional experiment, an arterial filter captured a significant number of microemboli at all flow rates. The Braile Infant oxygenator has a matched hemodynamic characteristic with the Quadrox‐i Pediatric oxygenator. The Quadrox‐i has a better GME handling ability compared with the Braile Infant oxygenator. Regardless of type of oxygenator an additional arterial filter decreases the number of GME.