Microfluidic systems can be simple and efficient devices for different applications in a wide variety of fields. Purification of specific cells, bacterium, or environmental particles are some examples of biomedical, biochemical, and industrial applications. This study aims to achieve an in silico and in vitro analysis of sedimentation pinched flow fractionation low-cost microfluidic system for size-based separation. To overcome the lack of polydispersity control in the preparation of polymeric microparticles as small-sized particles have greater advantages when it refers to drug-delivery and cell-mimicking. First, a Multiphysics simulation was carried out employing an Eulerian-Lagrangian approach for the prediction of particle sorting in the system. In this, a Flow Rate Ratio of 1:25, 3:100, and 1:50 and a Total Flow Rate of 0.0075 m/s were used. Then, chitosan microparticles between 1-20 µm were synthesized by the single-emulsion method to experimentally evaluate the results obtained in the simulations. In silico results showed that the microparticles were correctly isolated, with a difference in the size of approximately 5 µm between each outlet channel, there was no significant difference between the Flow Rate Ratios evaluated.