In addition to morphologic evaluation, cardiac computed tomography with a short scan time and a high spatial resolution may be performed to assess ventricular function in children with congenital heart disease, especially when cardiac magnetic resonance imaging is unavailable, inadequate, or contraindicated. Caution should be exercised over the computed tomography radiation dose because greater radiation doses are used to assess ventricular function than morphology. The three-dimensional threshold-based segmentation approach leads to higher accuracy and reproducibility of ventricular volumetry than the conventional approach, which frequently uses simplified contouring and two-dimensional disc summation. However, this approach is less frequently utilized in clinical practice than the conventional approach. Therefore, a step-by-step guide to cardiac computed tomography ventricular volumetry using three-dimensional threshold-based segmentation is presented for congenital heart disease.