The time constant of isovolumic relaxation is an established index of ventricular relaxation, a major component of diastolic function, even in a single right ventricle. However, the specific echocardiographic parameters for estimating diastolic dysfunction are insufficient for a single right ventricle. This study aimed to investigate the echocardiographic indices associated with time constant of isovolumic relaxation in post-Fontan operation patients with a single right ventricle. We included 39 patients with hypoplastic left heart syndrome after Fontan operation with an ejection fraction ≥45% and preserved valve function. First, the correlation between echocardiographic parameters and time constant of isovolumic relaxation was examined, and partial correlation coefficients were calculated using age and heart rate as covariates. Next, univariate regression analysis was performed using time constant of isovolumic relaxation as the objective variable and echocardiographic parameters as independent variables, followed by multivariate regression analysis incorporating parameters with p < 0.10. Among the echocardiographic parameters, global longitudinal strain correlated most strongly with time constant of isovolumic relaxation (r = 0.778, p < 0.001). This was consistent with the partial correlation coefficients (r = 0.707, p < 0.001). Using stepwise multivariate regression analysis, only global longitudinal strain was found to be an independent predictor of time constant of isovolumic relaxation (adjusted R2 = 0.551). Global longitudinal strain could be used as a surrogate marker of time constant of isovolumic relaxation, an invasive indicator of relaxation impairment, in post-Fontan operation patients with a single right ventricle, preserved ejection fraction, and valve function.