Manual blood exchange (MBE) is a leukoreduction therapy for hyperleukocytosis in Bordetella spp. We describe the impact of BE on clinical and biological parameters in critically ill children with malignant pertussis. This is a monocentric retrospective review of patients with malignant pertussis infection treated with MBE. It describes the evolution of haemodynamic, ventilatory, haematologic and metabolic characteristics before and after MBE. Between January 2006 and December 2021, nine patients (median age 43 days, range: 13-80 days) had 16 MBE for malignant pertussis. All patients were mechanically ventilated, and 7/9 patients developed pulmonary hypertension during their paediatric intensive care unit (PICU) stay. Overall, 3/9 patients survived, and the mean PICU length of stay was 8.5 days (range: 1-52 days). We found a significant reduction of the leukocyte count (pre-MBE: 61.8 G/L [interquartile range (IQR): 55.8-74.8] vs. post-MBE: 19.4 G/L [IQR: 17.7-24.1]; p ≤ 0.001) and significant oxygenation improvement (pre-MBE SpO2/FiO2: 190 [IQR: 106-200] vs. post-MBE SpO2/FiO2: 242 [IQR: 149-250]; p = 0.03). The main side effects were a significant reduction of thrombocytes (pre-MBE: 411 G/L [IQR: 166.5-563.5] vs. post-MBE: 66 G/L [IQR: 46-82.5]; p = <0.001) and of ionized calcium (iCa) (pre-MBE iCa: 1.3 [IQR: 1.22-1.37] vs. post-MBE iCa: 1.25 [IQR: 1.85-2.24]; p = 0.03). MBE efficiently reduces leukocytes and improves oxygenation in severe Bordetella pertussis infection in infants. Careful monitoring of calcium and thrombocytes seems mandatory.