Children with CHD have demonstrated a rise in obesity, and have unique risks related to comorbidities of obesity, including feeding dysfunction and exercise limitations. The incidence and cause of obesity among patients with surgically corrected CHD are not fully understood. This single-centre, longitudinal, retrospective cohort study identified patients between 2004 and 2020 with surgical correction. Diagnoses were restricted to d-transposition of the great arteries, coarctation of the aorta, or tetralogy of Fallot with surgical repair by 6 months of life without long-term post-operative complications or chromosomal abnormalities. Evaluation of Body Mass Index by survival curve for endpoints of overweight and obesity, as well as descriptive analysis of the population, was performed compared to the expected prevalence in the state of Oregon (13.7%). Cohorts were divided into eras in 5-year increments. Of 240 patients identified, 87 (36.2%) were overweight and 50 (20.8%) obese, findings significantly higher than expected prevalence (p = <0.01) for the same time period in the state of Oregon. Patients with coarctation of the aorta had a higher prevalence than other diagnoses (p = <0.01). Patients in the 2004–2008 cohort had the highest rates of obesity compared to other cohorts (p = <0.01 and p = <0.01, respectively), likely due to a longer observational period. However, the 2014–17 cohort had the highest rate of increase in hazard ratio. Children with surgically corrected CHD demonstrate higher prevalences of obesity compared to the general population. There is variation by diagnosis, with coarctation of the aorta having comparatively higher prevalences of obesity. Several factors may impact this discrepancy, including sports participation restrictions and initial emphasis on weight gain.