The percentage of shunt fraction significantly impacts the management of patients with congenital shunts, influencing strategic choices such as surgical or interventional procedures. This study compared the estimated shunt fraction (the ratio of pulmonary-to-systemic flow, Qp/Qs) for quantifying the left-to-right shunt in children with ventricular septal defect (VSD) using heart catheterization, four-dimensional (4D) flow, and two-dimensional (2D) flow magnetic resonance imaging (MRI). The goal was to establish a non-invasive and reliable measurement ratio between pulmonary and systemic blood flow in these patients. Between July 2022 and June 2023, patients scheduled to undergo invasive right heart catheterization were included in this study. MRI was performed one hour before the catheterization procedure. The correlation of shunt fraction was assessed between all methods after calculating the Qp/Qs ratio from 2D and 4D flow MRI and catheterization. A total of 24 patients (aged 3-15 years, eight females) were ultimately included in the study. The Qp/Qs ratios obtained from 4D flow had a robust correlation (correlation coefficient r = 0.962) compared to those obtained during catheterization. Cardiac catheterization recorded the mean shunt fraction at 1.499 ± 0.396, while 4D flow measured it at 1.403 ± 0.344, with no significant difference between the two techniques. Moreover, there was a reasonable correlation (r = 0.894) between 2D flow measurements of Qp/Qs and the results obtained from catheterization, with a mean shunt fraction of 1.326 ± 0.283. 4D flow MRI has the potential to be a non-invasive method for accurately measuring the left-to-right shunt in children with VSD.