Extracorporeal life support (ECLS) is a widely used lifesaving technology. Whether ECLS results in immune dysregulation is unclear. This study’s aim was to examine whether ECLS affected innate immune response. All patients placed on ECLS were eligible. Blood was obtained before, during, and after ECLS. Function of the innate immune system was measured by ex vivo lipopolysaccharide (LPS)-induced tumor necrosis factor-α (TNF-α) and plasma cytokine levels (interleukin [IL]-6, IL-8, IL-10, and TNF-α). Immunoparalysis was defined as ex vivo TNF-α levels less than 200 pg/ml. Nineteen patients were enrolled with twelve <18 years old. Median ECLS duration was 10 days (range: 3–108); nine patients died. After stratifying the cohort by the presence of immunoparalysis before ECLS, those immunoparalyzed showed increased response to LPS on days 1 and 3 (p = 0.016). Those without pre-ECLS immunoparalysis showed a transient decrease in response on day 3 (p = 0.008). Plasma IL-10 levels were elevated in those with pre-ECLS immunoparalysis and dropped significantly by day 1 (p = 0.031). The number treated with steroids was similar in the two groups. In conclusion, patients with immunoparalysis before ECLS showed a gradual increase in immune function during ECLS, whereas those without immunoparalysis had a transient decrease in responsiveness on day 3.