In this paper, we propose to use the eikonal equation as a boundary condition when advective or normal flow equations in the level set formulation are solved numerically on polyhedral meshes in the three-dimensional domain. Since the level set method can use a signed distance function as an initial condition, the eikonal equation on the boundary is a suitable choice at the initial time. Enforcing the eikonal equation on the boundary for later times can eliminate the need for inflow boundary conditions, which are typically required for transport equations. In selected examples where exact solutions are available, we compare the proposed method with the method using the exact Dirichlet boundary condition. The numerical results confirm that the use of the eikonal boundary condition provides comparable accuracy and robustness in surface evolution compared to the use of the exact Dirichlet boundary condition, which is generally not available. We also present numerical results of evolving a general closed surface.