Abstract This paper presents the theory and development, validation, and results of a transient computational multiphysics model for analyzing the magnetic field, particle dynamics, and capture efficiency of magnetic and nonmagnetic (e.g., Red Blood Cells and E. Coli bacteria) microparticles in a traveling wave ferromagnetic microfluidic device. This computational model demonstrates proof-of-concept of a method for greatly enhancing magnetic bioseparation in ferromicrofluidic systems using an array of copper conductive elements arranged in quadrature to create a periodic potential energy landscape. In contrast to previous works, our approach theoretically uses a microfluidic device with an electronic chip platform consisting of integrated copper electrodes that carry currents to generate programable magnetic field gradients locally. Alternating currents are applied to the electrodes in quadrature (using a 90 deg phase change from the neighboring electrode) to create a periodic magnetic field pattern that travels along the length of the microchannel. Our previous work evaluated magnetic and nonmagnetic particles in a static magnetic field within the same channel geometry. This work is a phase 2 study that expands on the previous work and analyzes the dynamics of magnetic and nonmagnetic entities characterized by material magnetic susceptibility in a transient magnetic field. This is an improvement over our previous work. The model, which is described in more detail in the methods section, combines a Eulerian-Lagrangian and two-way particle-fluid coupling CFD analysis with closed-form magnetic field analysis that is used to predict magnetic separation considering dominant magnetic and hydrodynamic forces similar to our previous works in magnetic drug targeting. The model was also validated with an experimental low frequency stationary flow study on separating nonmagnetic latex fluorescent particles in a water based ferrofluid. The results from the experimental study and the developed model demonstrate that the proposed device may potentially be used as an effective platform for microparticle and cellular manipulation and sorting. The developed multiphysics model could potentially be used as a design optimization tool for traveling wave ferromicrofluidic devices.