We aimed to investigate plasma connective tissue growth factor (CTGF) levels in pulmonary arterial hypertension (PAH) associated with congenital heart disease (CHD) (PAH–CHD) in children and the relationships of CTGF with hemodynamic parameters. Plasma CTGF levels were calculated in 30 children with CHD, 30 children with PAH–CHD and 25 health volunteers, using the subtraction method. Cardiac catheterization was performed to measure clinical hemodynamic parameters. Plasma CTGF levels were significantly higher in PAH–CHD than in those with CHD and health volunteers (p < 0.01). In cyanotic PAH–CHD, plasma CTGF levels were significantly elevated compared with acyanotic PAH–CHD in the same group (p < 0.05). Plasma CTGF levels showed positive correlation with B-type natriuretic peptide (BNP) in PAH–CHD (r = 0.475, p < 0.01), while oxygen saturation was inversely related to plasma CTGF levels (r = −0.436, p < 0.05). There was no correlation between CTGF and hemodynamic parameters. Even though the addition of CTGF to BNP did not significantly increase area under curve for diagnosis of PAH–CHD compared with BNP alone (p > 0.05), it revealed a moderately better specificity, positive predictive value and positive likelihood ratio than BNP alone. Plasma CTGF levels could be a promising diagnostic biomarker for PAH–CHD in children.