ABSTRACT This study presents an investigation of an innovative microfluidic flow separator using both numerical and experimental approaches to calibrate contrast‐enhanced ultrasound scanners. Numerical simulations were conducted using Lagrangian particles tracking and passive scalar transport methodologies using the OpenFOAM software. The experimental validation confirmed the accuracy of the numerical simulations, particularly at an imposed total pressure of , showing an excellent agreement in particle distributions. The study emphasizes the computational efficiency and modeling of passive scalar transport, providing valuable understanding into the behavior of scalar quantities in microfluidic systems. An optimized diffusion coefficient value of was identified, showing its critical role in achieving accurate simulation results and optimizing the performance of microfluidic flow separators for contrast‐enhanced ultrasound scanner calibration.