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Lymphopenia is common in patients with Fontan circulation and no history of protein‐losing enteropathy, but this phenomenon has not been significantly described in the literature. We retrospectively identified patients with Fontan circulation who underwent catheterization between January 2003 and January 2013 at our center. Patients who had complete blood count with differential drawn within 12 months of the catheterization were included. Patients were excluded if complete blood count with differential was drawn in setting of possible infection or if there was history of protein‐losing enteropathy (PLE). Possible associations between patient characteristics and absolute lymphocyte count (ALC) were examined. Fifteen patients were included. The median age at catheterization was 10.2 years (3.8–26.9) and median time from Fontan operation was 6.5 years (0.7–22.1). Twelve (80%) patients had undergone extracardiac Fontan and 9 (60%) had fenestration placed. The median time between complete blood count with differential and catheterization was 2 days (0–346). The median inferior vena cava (IVC) pressure was 13 mm Hg (7–20). The median ALC was 1.5 × 103/μL (0.8–4.5). Four patients (26.7%) met criteria for lymphopenia with ALC < lower limit of normal and 7 (46.7%) patients had an ALC ≤ lower limit of normal. ALC was not associated with any hemodynamic variables but was associated with platelet count (rho = 0.5, P= .04), total white blood cell count (rho = 0.8, P≤ .001), and absolute monocyte count (0.7, P= .002). In a cohort of patients with Fontan circulation and no history of protein‐losing enteropathy who underwent catheterization, lymphopenia was common and positively associated with low platelet count. Thrombocytopenia has been shown to correlate with the degree of hepatic fibrosis in those with Fontan and, thus, hepatic fibrosis may underlie lymphopenia in these patients.