The present invention relates to a method of manufacturing a vertically-structured GaN-based light emitting diode. The method of manufacturing a vertically-structured GaN-based light emitting diode includes forming a GaN layer on a substrate; patterning the compound layer in a predetermined shape; forming an n-type GaN layer on the patterned compound layer through the epitaxial lateral over-growth process and sequentially forming an active layer and a p-type GaN layer on the n-type GaN layer; forming a structure supporting layer on the p-type GaN layer; sequentially removing the substrate and the GaN layer formed on the substrate after forming the structure supporting layer; removing the patterned compound layer exposed after removing the GaN layer so as to form an n-type GaN layer patterned in a concave shape; and forming an n-type electrode on the n-type GaN layer patterned in a concave shape.