We present an experimental and theoretical analysis of dielectrophoretic (DEP) particle deflection in a microfluidic channel for the separation of protein-bound particles. A 2D electrode array with widely spaced bars is designed to deflect a particle at the exit of the fluidic channel by negative DEP force. When particles pass through the channel, the particle streams are deflected differently depending on the DEP characteristics of the particles. In this paper, we propose methodologies to characterize the DEP force with the deflection distance using comparative analyses of a simulation and an experiment. The deflection distances of the particles are measured as a function of the ac voltage applied and compared with full 3D simulations. The Clausius–Mossotti (CM) factor of a protein-bound particle is analyzed, based on frequency-dependent deflection distance data measured experimentally, and protein-bound particles are separated from a mixture with nonbound particles in a real application. Two particle groups, 2.3 µm and 6.4 µm polystyrene particles, were used for the simulation and experimental study, and the 6.4 µm diameter particles were selected as an adequate protein-binding substrate for the application of biomolecular detection. Bovine serum albumin (BSA) was used as a test target protein. The particle's BSA binding is identified by the change in the particle's deflection distance. In particular, we used 1 wt% BSA as a target protein sample to investigate the deflection of 6.4 µm diameter particles as a function of protein concentration. The frequency-dependent CM factor curves for BSA-bound and nonbound particles are also calculated theoretically. Therefore, this paper shows a model analytic study on the biomolecular detection performance of a fabricated DEP-deflection microsystem. In addition, we present further significant analyses such as calculation of the electrical surface conductance of BSA around a particle, and we trace simulation errors. The surface conductance of particles treated with 1 wt% BSA was calculated to be 1.36 nS.