This paper presents the properties of GaN p-n junction grown on a Si substrate by molecular beam epitaxy (MBE) at different annealing temperatures. The samples were annealed using conventional furnace annealing. The effects of thermal annealing on the samples were observed via X-ray diffraction (XRD), atomic force microscopy (AFM), photoluminescence (PL), current-voltage (I-V) and energy dispersive X-ray (EDX) measurements. From the measurements, the optimum annealing temperature was found to be 1,000°C, which gave the sample the best crystal quality. However, the optimum sample showed poor electrical characteristics due to the diffusion of Si atoms from the substrate towards the p-GaN layer. This effect was more significant for the samples annealed above 1,000°C.