Arbuscular mycorrhizal (AM) fungi and endophytic fungi collectively symbiose well with plants and, thus, stimulate plant growth; however, it is not clear whether field inoculation of the fungi enhances the resistance potential of plants, particularly in citrus. In the present study, we inoculated AM fungi (Acaulospora scrobiculata, Diversispora spurca, and D. versiformis) and endophytic fungi (Piriformospora indica) on an eight-year-old lane late navel orange (Citrus sinensis (L.) Osb) trees grafted on Poncirus trifoliata in a field, and we analyzed the response of the leaf antioxidant defense system. Approximately 2 years after inoculation, the root fungal colonization rate and soil hyphal length significantly increased. Fungal inoculation significantly increased the activity of leaf antioxidant enzymes, such as superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase, and the content of non-enzymatic antioxidants, such as reduced ascorbic acid and reduced glutathione. As a result, fungi-inoculated plants maintained lower concentrations of hydrogen peroxide and superoxide anion radicals and lower levels of membrane lipid peroxidation (according to malondialdehyde level) in leaves than uninoculated plants. Among them, inoculation of D. spurca and A. scrobiculata showed relatively higher effects in enhancing the antioxidant defense system than the other fungi. Furthermore, inoculation of D. spurca induced expressions of CsFe-SOD, CsMn-SOD, CsPOD, CsCAT1, and CsPRR7; inoculation of A. scrobiculata and D. versiformis induced expressions of CsCAT1; CsCAT1 and CsPOD were also induced by inoculation of P. indica. All four inoculations almost upregulated expressions of CsFAD6. AM fungi had superior effects than endophytic fungi (e.g., P. indica). According to our findings, inoculation with beneficial fungi, specifically mycorrhizal fungus D. spurca, activated the antioxidant defense system of field citrus trees, thus, having potentially superior resistance in inoculated plants.