To assess a two-phase contrast injection protocol for contrast enhancement during cardiac computed tomography (CT) in children with congenital heart disease. Forty-three children (20 boys, 23 girls) of median age 13 months (range 3 days—8.3 years) and weighing ≤ 20 kg who underwent cardiac CT using a two-phase contrast injection protocol at our institution were retrospectively identified. High-pitch spiral third-generation dual-source cardiac CT (tube voltage 70 kV) was performed with a fixed delay of 60 s after contrast injection in the order of 10 mgI/kg/s (30 s), 15 mgI/kg/s (20 s), and a saline chaser (10 s). Attenuation in the inferior vena cava (IVC), superior vena cava (SVC), right atrium (RA), right ventricle (RV), pulmonary artery (PA), left atrium (LA), left ventricle (LV), and descending aorta (AO) was compared using the Steel–Dwass and Fisher’s exact tests. The median (interquartile range) attenuation in the IVC, SVC, RA, RV, PA, LA, LV, and AO was 285 (264–347) Hounsfield units (HU), 416 (370–445) HU, 368 (320–388) HU, 373 (322–417) HU, 397 (330–432) HU, 425 (373–469) HU, 435 (385–468) HU, and 437 (392–491) HU, respectively (p < 0.05, IVC vs. the other anatomic sites). There was no significant difference in diagnostic success rate for attenuation > 250 HU between the IVC (41 children, 95.3%) and the other sites (43 children, 100%). A two-phase contrast injection protocol is useful for effective contrast enhancement in pediatric cardiac CT.