The present invention provides a fuel cell separator and a method for surface treatment of the same, in which ionized nanoparticles are attached to the surface of a separator to form fine projections such that the surface of the separator exhibits superhydrophobicity. For this purpose, the present invention provides a method for surface treatment of a fuel cell separator which provides nanoparticles for forming fine projections on the surface of the separator to a discharge electrode and ionizes the nanoparticles by an arc discharge generated in the discharge electrode. The ionized nanoparticles are then attached to the surface of the separator by an electric field generated by applying a high voltage between the separator and the discharge electrode, thereby forming fine projections for imparting superhydrophobicity.