Background Fluid overload associates with poor outcomes after neonatal cardiac surgery, but consensus does not exist for the most clinically relevant method of measuring fluid balance (FB). While weight change-based FB (FB-W) is standard in neonatal intensive care units, weighing infants after cardiac surgery may be challenging. We aimed to identify characteristics associated with obtaining weights and to understand how intake/output-based FB (FB-IO) and FB-W compare in the early postoperative period in this population. Methods Observational retrospective study of 2235 neonates undergoing cardiac surgery from 22 hospitals comprising the NEonatal and Pediatric Heart and Renal Outcomes Network (NEPHRON) database. Results Forty-five percent ( n  = 998) of patients were weighed on postoperative day (POD) 2, varying from 2 to 98% among centers. Odds of being weighed were lower for STAT categories 4 and 5 (OR 0.72; 95% CI 0.53–0.98), cardiopulmonary bypass (0.59; 0.42–0.83), delayed sternal closure (0.27; 0.19–0.38), prophylactic peritoneal dialysis use (0.58; 0.34–0.99), and mechanical ventilation on POD 2 (0.23; 0.16–0.33). Correlation between FB-IO and FB-W was weak for every POD 1–6 and within the entire cohort (correlation coefficient 0.15; 95% CI 0.12–0.17). FB-W measured higher than paired FB-IO (mean bias 12.5%; 95% CI 11.6–13.4%) with wide 95% limits of agreement (− 15.4–40.4%). Conclusions Weighing neonates early after cardiac surgery is uncommon, with significant practice variation among centers. Patients with increased severity of illness are less likely to be weighed. FB-W and FB-IO have weak correlation, and further study is needed to determine which cumulative FB metric most associates with adverse outcomes. Graphical abstract A higher resolution version of the Graphical abstract is available as Supplementary information .