We present the first characterization of multiple organ dysfunction (OD) patterns and their associations with in-hospital mortality for children on extracorporeal membrane oxygenation (ECMO). We retrospectively assessed OD for 317 children on ECMO support at a single center between 2011 and 2024. Organ dysfunction was calculated in 24 hour intervals using Pediatric Organ Dysfunction Information Update Mandate (PODIUM) criteria, as well as Pediatric Sequential Organ Failure Assessment (pSOFA) and Pediatric Logistic Organ Dysfunction-2 (PELOD-2) scores. Multiple logistic regression and survival analyses observed the same pattern; there was no difference in the number of concurrent PODIUM ODs between survivors and non-survivors before cannulation. However, starting as early as the day of cannulation, an accumulation of more ODs developed in non-survivors (median of 7 ODs [interquartile range {IQR}: 6–8]) as compared to survivors (6 [IQR: 5–7], p < 0.001). This difference persisted throughout the ECMO course and further widened after decannulation. Pediatric Sequential Organ Failure Assessment and PELOD-2 scores followed the same pattern and were significantly different between the two groups. Because differences in the number of concurrent ODs between survivors and non-survivors only began to emerge shortly after cannulation, this suggests that identifying intervenable risk factors before and peri-cannulation could change the trajectory of multiple OD and mortality risk.