Sarcopenia is an increasingly recognized marker of frailty in cardiac patients. Patients with a history of congenital heart disease and Fontan procedure have a higher risk of developing progressive muscle wasting. Our objective was to determine if we could use routine cardiac MRI (CMR) for the surveillance of muscle wasting. A retrospective study of all Fontan patients (n = 75) was conducted at our institution, with CMR performed from 2010 to 2022 and exercise stress testing performed within 12 months (4.3 ± 4.2 months). The skeletal muscle area (SMA) for the posterior paraspinal and anterior thoracic muscles were traced and indexed for body surface area (BSA). Patients were stratified by percentile into the upper and lower quartiles, and the two groups were compared. Multivariable regression was performed to control for sex and age. There was a significant positive association of both anterior (r = 0.34, = 0.039) and paraspinal (r = 0.43, = 0.007) SMA to peak VO . Similarly, paraspinal but not anterior SMA was negatively associated with the V /V (r = -0.45, = 0.006). The upper quartile group had significantly more males (18/19 vs. 8/20; = 0.0003) and demonstrated a significantly higher peak VO (32.2 ± 8.5 vs. 23.8 ± 4.7, = 0.009), a higher peak RER (1.2 ± 0.1 vs. 1.1 ± 0.04, = 0.007), and a significantly lower V /V (32.9 ± 3.6 vs. 40.2 ± 6.2, = 0.006) compared to the lowest quartile. The association of SMA to VO peak and V /V was redemonstrated after controlling for sex and age. Thoracic skeletal muscle area may be an effective surrogate of muscle mass and is correlated to several measures of cardiorespiratory fitness post-Fontan. CMR would be an effective tool for the surveillance of sarcopenia in post-Fontan patients given its accessibility and routine use in these patients.