<p>Socioeconomic disadvantage is linked to adverse outcomes after congenital cardiac surgery, but its long-term link is unclear. Single-center retrospective analysis of individuals who underwent cardiac surgery from 2007 to 2022 measured the association of socioeconomic status and late mortality (any post-discharge death at least 30 days after initial surgery). Mortality was determined by electronic health records and the National Death Index. Socioeconomic status was based on patients’ neighborhood Child Opportunity Index (COI) score. The lowest two COI quintile neighborhoods were designated “disadvantaged” while the highest two were designated “advantaged.” Multivariable mixed model analyses measured the strength of association between socioeconomic status and mortality, adjusting for STAT category, demographic, and clinical factors. Of the 2546 patients, half (49%, <i>n</i> = 1,235) were from disadvantaged neighborhoods. One third (31%, <i>n</i> = 787) were considered advantaged. Compared to patients from advantaged neighborhoods, patients from disadvantaged neighborhoods suffered greater overall mortality (14% vs. 8%, <i>p</i> &lt; 0.001), more frequent complications (14% vs. 10%, <i>p</i> &lt; 0.001), more genetic syndromes (23% vs. 19%, <i>p</i> = 0.021), and were smaller at surgery (5.15&#xa0;kg vs. 5.60&#xa0;kg, <i>p</i> = 0.006). Multivariable analysis adjusting for STAT category, prematurity, weight at surgery, and genetic syndromes found patients from disadvantaged neighborhoods had greater overall mortality (aOR:1.52; CI 1.10–2.12, <i>p</i> = 0.013). Genetic syndromes and weight at surgery were associated with increased overall mortality (aOR:1.60; CI 1.17–2.20, <i>p</i> = 0.004, aOR: 0.66; CI 0.53–0.81, <i>p</i> &lt; 0.001, respectively). Patients from disadvantaged neighborhoods carry greater risk of mortality after congenital cardiac surgery. The relationship between socioeconomic status and mortality may be mediated by weight and genetic syndromes.</p>