Bone-specific alkaline phosphatase (BALP) is produced by osteoblasts. A recent series noted a positive association between cardiac index (CI) and BALP in patients with Fontan circulation. CI is low at baseline in these patients, and small decreases in CI may result in diverting of blood away from bone. We prospectively enrolled 15 patients (males ≤ 14 yo, females ≤ 12 yo) who had previously undergone Fontan operation and were undergoing cardiac catheterization. Serum BALP was measured at catheterization, and analysis performed to evaluate association between age-/gender-specific BALP z-score and CI as well as other patient variables. The median age at catheterization was 5.6 years (3.1–13.1), and time from Fontan was 1.5 years (0.1–12.1). The median superior vena cava saturation (SVC) was 65 % (52–74), median average between SVC and inferior vena cava (IVC) saturations was 62.5 % (51–70), and median CI was 3.8 L/min/m² (2.0–8.4). The median BALP was 65 IU/L and BALP z-score was −2.1 (−3.2 to 0.9). BALP z-score was not associated with CI (ρ = −0.1, p = 0.7), but a positive correlation was noted with the average of SVC and IVC saturation (ρ = 0.5, p = 0.052) and with SVC saturation (ρ = 0.4, p = 0.07), both nearly reaching statistical significance. In our cohort of children with Fontan circulation undergoing catheterization, BALP z-score was not associated with CI, but an association with estimates of mixed venous saturation was noted that nearly reached statistical significance. We hypothesize that BALP is a marker of oxygen delivery in those with Fontan circulation and may represent a valuable biomarker in this population.