The growth parameter dependence of structural, electrical and magnetic properties in Gd-doped GaN layers grown by plasma-assisted molecular beam epitaxy has been investigated. The structural and magnetic properties of Gd-doped GaN films grown on GaN templates strongly depend on the MBE growth condition. While Gd-doped GaN grown under relatively high Ga fluxes consist of wurtzite GaGdN layers without Gd-related precipitates, Gd-incorporated GaN films grown under low Ga fluxes contain a lot of nanoparticles ranging from several nm to several tens nm in size. The samples with Gd-related nanoparticles exhibit hysteresis in the magnetization–magnetic field curves at 10K. The separation between the field-cooled and zero-field-cooled magnetization–temperature curves is observed at around 30K. This behavior is understood in terms of super-paramagnetism originating from the ferromagnetic nanoparticles observed in the cross-sectional transmission electron microscopy images.