This study aimed to assess whether the proinflammatory markers procalcitonin (PCT), C-reactive protein (CRP), or interleukin 6 (IL-6) are associated with mortality in neonates with congenital diaphragmatic hernia (CDH) requiring extracorporeal membrane oxygenation (ECMO). Congenital diaphragmatic hernia neonates receiving venovenous ECMO between December 2012 and June 2022 were retrospectively reviewed and grouped by survival status. Longitudinal CRP, PCT, and IL-6 levels during the first 10 days on ECMO were analyzed using the Mann-Whitney U test. A PCT cut-off was determined to define a “high inflammatory response group,” further evaluated with Kaplan-Meier curves and the log-rank test. Independent mortality risk factors were identified using Cox regression. Among nonsurvivors, PCT values were significantly higher on day 2 (p = 0.028), day 3 (p = 0.028), day 6 (p = 0.031), and day 10 (p = 0.017) after ECMO initiation. Infants in the high inflammatory response group had significantly shorter survival time (p = 0.006). C-Reactive protein and IL-6 were not significantly associated with mortality. In multivariable Cox regression analysis, high PCT on day 2 of ECMO (hazard ratio: 1.022; 95% confidence interval [CI]: 1.004–1.040) and severe pulmonary hypertension (hazard ratio: 3.270; 95% CI: 1.245–8.588) were independently associated with mortality. High PCT in CDH neonates receiving ECMO is significantly associated with increased mortality and reduced survival time.