The non-Abelian Berry phase is an essential feature of non-Abelian anyons for the realization of topological quantum computation. This thesis is primarily a study about the numerical calculation of the Berry phase of non-Abelian anyons in the Kitaev honeycomb lattice model. It is also a guide for experimental the realizations of the actual brading process. We give an introduction to the theory of non-Abelian anyons, briefly discussing in what kind of systems they are realized, and their possible use in topological quantum computation. Non-Abelian anyons are studied within the Kitaev honeycomb model where they are realized on the plaquettes of the honeycomb lattice. The Kitaev honeycomb model can be solved exactly by using various fermionization methods. In this thesis, we review a solution based on Jordan-Wigner types of fermions which transform Hamiltonian to a fermionic quadratic form. This kind of fermionization procedure is quite general and can be applied to any trivalent spin lattice models. Moreover, we introduce Hartree-Fock-Bogoliubov method to solve general quadratic fermionic Hamiltonian and employ Bloch-Messiah theorem in order to write ground state wave function explicitly. Later, we apply these methods to honeycomb model and study the eigenstates of the model so that we can do the Berry phase calculation. The final chapter explains the details of the numerical calculation of the non-Abelian Berry phase. First, we show how to create and adiabatically move vortices in the honeycomb model. A brief review of the Berry phase is given including some discussion about a numerical approach. Later on Thouless’ representation of the ground state is introduced to calculate the Berry phase. All these theoretical tools are applied to a 4 vortex configuration of the model to calculate the non-Abelian Berry phase of the system on a particular path in the parameter space.