The early stage degradation of electrical properties in AlGaN/GaN high electron mobility transistors (HEMTs) under fast neutron irradiation is studied. After the 1 MeV neutron irradiation at a low fluence of 1 × 1014 neutrons/cm2, the reverse leakage current decreases while the output and transfer characteristics remain unchanged, which cannot be explained by the previously reported high-fluence degradation model. By employing temperature-dependent gate leakage current measurements, we show that the dislocation related Poole-Frenkel (PF) emission dominates the gate leakage mechanism before and after irradiation whereas the barrier height for electron emission to conductive dislocation increases after the neutron irradiation. A model with the evolution of dislocation from the VGa-decorated configuration to the pure configuration is proposed to describe the degradation of AlGaN/GaN HEMTs at the low-fluence early stage neutron irradiation. This model enriches the understanding of the degradation mechanism of neutron irradiated AlGaN/GaN HEMTs.