Neonatal fluid management in extracorporeal life support (ECLS) is complex, with the goal of improving outcomes while preventing complications. This study evaluates the impact of early continuous renal replacement therapy (CRRT) on volume status, outcomes, and renal recovery in neonatal ECLS. A single-center retrospective review of neonates was performed (2007–2023, n =108). Routine early CRRT began in 2011, providing a natural cohort comparison between early (≤48 hours) and delayed/no CRRT. Early (70.4%) and delayed/no (29.6%) CRRT cohorts had similar ECLS indications, birthweights, and mortality. Time from cannulation to CRRT initiation was 4 hours (early CRRT) versus 4.4 days (delayed CRRT) (p < 0.001). Early CRRT was associated with significantly reduced median peak fluid balance (30% vs. 37%, p < 0.05) and earlier negative volume status, with 80% achieving negative fluid balance by day 3, compared with 53% in the delayed group (p = 0.030). In survivors, early CRRT had significantly shorter ECLS runs (5.1 vs. 8.6 days, p < 0.001) with fewer median extrarenal ECLS complications (1.0 vs. 3.0, p = 0.001). No differences were observed in renal recovery. Though the study design prohibits definitive conclusions, early CRRT initiation in neonatal ECLS was associated with improvement in early and peak fluid balance status and reduced ECLS duration and complications without differences in long-term renal outcomes.