This paper presents a three-dimensional simulation of a micro hydrocyclone for the separation of micron sized particles from liquid in a particulated sample. A theoretical analysis is performed to demonstrate the working principle of the micro hydrocyclone and develop design models. The geometry of the proposed device is designed based on the Bradley model, since it offers a lower cut-size, thus making it suitable for microfluidics applications. The operational parameters of the hydrocyclone are derived from a dimensional group model. The particle separation process inside the micro hydrocyclone is simulated by solving fluid flows using Navier-Stokes equations and particle dynamics using the Lagrangian approach in a Eulerean fluid. First, the numerical model is validated by comparing the simulation results with the experimental results for a macroscale hydrocyclone reported in the literature. Then, the micro hydrocyclone is simulated and the simulation results are presented and discussed in the context of the functioning of the micro hydrocyclone. Finally, the effects of inlet velocity, vortex finder diameter, particle size, and density on the separation efficiency are investigated. The proposed device can be easily integrated with micro-environments; thus, is suitable for lab-on-chip and microsystems development.