We have investigated effects of the rapid thermal annealing of GaN epilayers by molecular beam epitaxy in nitrogen atmosphere. The improvement of structural properties of the samples was observed after rapid thermal annealing under optimum conditions. This improvement in crystal quality is due to a reduction of the spread in the lattice parameter in epilayers. The annealing has been performed in a rapid thermal annealing furnace at $950^{circ}C$. The effect of rapid thermal annealing on the structural properties of GaN was studied by x-ray diffraction. The Bragg peak shifts toward larger angle as the annealing time increases. As the thermal treatment time increases, FWHM(full width at half maximum) of the peak slightly increase with its decreases followed and it increases again. Results demonstrate that rapid thermal annealing did not always promote qualities of GaN epilayers. However, rapid thermal annealing under optimum conditions improve structural properties of the samples, elevating their crystal quality with a reduction of inaccuracy in the lattice parameter of the epilayers.