Various late complications are associated with the Fontan procedure. In patients who undergo the Fontan procedure, the central venous pressure (CVP) tends to be higher than normal. However, the relationship between CVP (at rest and during exercise) and late complications associated with the Fontan procedure is unknown. Thirty-four patients who underwent the Fontan procedure were enrolled in this study. The median age was 19.3 years, and the median time after the Fontan procedure was 12.7 years. With exercise, the CVP increased from a median of 11 to 19 mmHg, and the cardiac index increased from a median of 2.1 to 4.4 l/min/m². In 38% of the patients, CVP measured at the resting condition and during exercise differed. Laboratory results indicated no significant difference between the patients in the high-CVP group and low-CVP group at rest. In contrast, during exercise, brain natriuretic peptide (67 ± 38 vs. 147 ± 122 pg/ml, p < 0.05), gamma-glutamyl transpeptidase (63 ± 33 vs. 114 ± 30 IU/l, p < 0.05), type IV collagen 7S (6.7 ± 1.3 vs. 8.1 ± 1.3 ng/ml, p < 0.05), and creatinine (0.72 ± 3.14 vs. 0.83 ± 3.16 mg/dl, p < 0.05) levels were significantly higher in the high-CVP group than in the low-CVP group. Elevated CVP during exercise may be associated with long-term complications after the Fontan procedure; hence, CVP should be measured during exercise in patients who underwent the Fontan procedure to accurately predict the risk of developing such complications.