In this study, p-side-up GaN-based light-emitting diodes (LEDs) with textured indium-tin oxide (ITO) or silicon dioxide (SiO2) surface layers were investigated by natural lithography using polystyrene spheres (PSs) as an etching mask. It was found that the ITO top layer provides better roughness than SiO2. Under the optimum surface treatment parameter, the roughnesses of textured ITO and SiO2 surface layers are 140 nm and 15 nm, respectively. The diameter of PSs in the textured ITO surface is still maintained at about 250–300 nm. Correspondingly, the size of PSs in the SiO2 surface is reduced to about 100 nm. The output powers of LEDs with textured ITO and SiO2 surfaces and conventional LEDs are 10.9, 9.5, and 8.5 mW at 20 mA, respectively. LEDs fabricated using the textured ITO surface produced an output power that exceeded that of planar-surface LEDs by about 28% at 20 mA dc current.