Strain plays an important role in the performance and reliability of AlGaN/GaN high electron mobility transistors (HEMTs). However, the impact of strain on the performance of proton irradiated GaN HEMTs is yet unknown. In this study, we investigated the effects of strain relaxation on the properties of proton irradiated AlGaN/GaN HEMTs. Controlled strain relief is achieved locally using the substrate micro-trench technique. The strain relieved devices experienced a relatively smaller increase of strain after 5 MeV proton irradiation at a fluence of 5 × 1014 cm−2 compared to the non-strain relieved devices, i.e., the pristine devices. After proton irradiation, both pristine and strain relieved devices demonstrate a reduction of drain saturation current (Ids,sat), maximum transconductance (Gm), carrier density (ns), and mobility (μn). Depending on the bias conditions the pristine devices exhibit up to 32% reduction of Ids,sat, 38% reduction of Gm, 15% reduction of ns, and 48% reduction of μn values. In contrast, the strain relieved devices show only up to 13% reduction of Ids,sat, 11% reduction of Gm, 9% reduction of ns, and 30% reduction of μn values. In addition, the locally strain relieved devices show smaller positive shift of threshold voltage compared to the pristine devices after proton irradiation. The less detrimental impact of proton irradiation on the transport properties of strain relieved devices could be attributed to reduced point defect density producing lower trap center densities, and evolution of lower operation related stresses due to lower initial residual strain.