The variation in ferromagnetism caused by position-specific point defects in GaN (100 nm) thin films is reported here. We observe a systematic variation of magnetic properties in GaN films after 300 KeV Xe+ ion irradiation with different fluences, i.e., 5 × 1012, 5 × 1013, and 5 × 1014 ions-cm−2. Metal Organic Chemical Vapor Deposition (MOCVD) grown Pristine GaN thin film contains Ga vacancies and related defects (as analysed by photoluminescence study) and shows a magnetic moment of ∼ 0.99 emu/g at room temperature. The GaN (002) peak intensity in XRD data decreases with increasing irradiation fluences, confirming that both Ga and N have been removed from their lattice sites and that the content of both Ga and N in irradiated samples has been reduced compared to the as-deposited one. It is evident from the PL data that Ga vacancy-type defects are maximum in pristine samples, after ion beam irradiation the appearance of some new peaks in the photoluminescence data indicates the creation of some new types of defects. The XPS data (Ga 3d and N 1s) also reveals that the intensity of the peak corresponding to Ga bonded with N decreases with higher irradiation doses. This reveals that Ga and N content have been decreased after ion irradiation. The orderly decrease of magnetic moment with increasing ion fluence is possibly due to the isolated Ga vacancies in the pristine film as it has the minimum formation energy and maximum magnetic moment as evident from Density Functional Theory (DFT) results. Therefore, the pristine GaN shows the maximum magnetic moment and, after ion beam irradiation, the creation of Ga vacancies at adjacent sites and other point defects is favourable as pristine GaN already contains Ga vacancies at random sites. DFT results further show that the magnetic moment decreases for other defect configurations rather than the isolated Ga vacancies.