A method of manufacturing a vertical GaN-based LED includes forming a nitride-based buffer layer on a silicon substrate; sequentially forming a p-type GaN layer, an active layer, and an n-type GaN layer on the nitride-based buffer layer; forming an n-electrode on the n-type GaN layer; forming a plating seed layer on the n-electrode; forming a structure supporting layer on the plating seed layer; removing the silicon substrate through wet etching and forming roughness on the surface of the p-type GaN layer through over-etching; and forming a p-electrode on the p-type GaN layer having the roughness formed.