Refractory right ventricular failure has significant morbidity and mortality. Extracorporeal membrane oxygenation is indicated when medical interventions are deemed ineffective. However, it is still being determined if one configuration is better. We conducted a retrospective analysis of our institutional experience comparing the peripheral veno-pulmonary artery (V-PA) configuration versus the dual-lumen cannula with the tip in the pulmonary artery (C-PA). The analysis of a cohort of 24 patients (12 patients in each group). There was no difference in survival after hospital discharge (58.3% in the C-PA group compared to 41.7% in the V-PA group, p = 0.4). Among the C-PA group, there was a statistically significant shorter ICU length of stay (23.5 days [interquartile range {IQR} = 19–38.5] vs. 43 days [IQR = 30–50], p = 0.043) and duration of mechanical ventilation (7.5 days [IQR = 4.5–9.5] compared to (16.5 days [IQR = 9.5–22.5], p = 0.006) in the V-PA group. In the C-PA group, there were lower incidents of bleeding (33.33% vs. 83.33%, p =0.036) and combined ischemic events (0 vs. 41.67%, p = 0.037). In our single-center experience, the C-PA configuration might have a better outcome than the V-PA one. Further studies are needed to confirm our findings.