<p>The bacterium <i>Xanthomonas citri</i> subsp. <i>citri</i> (Xcc), which causes citrus canker disease, has caused great harm to citrus production worldwide. In this study, we aimed to clarify the antibacterial activities of extracts prepared with solvents of different polarities from the fungus <i>Nemania</i> sp. LJZ-Y-11 against Xcc, isolate and identify the active secondary metabolites, as well as evaluate the effects of the active compound on the Xcc. The results showed that extracts displayed significant antibacterial activities with the minimum inhibitory concentrations (MICs) and the minimal bactericidal concentrations (MBCs) at 0.3125 − 5 mg.mL⁻¹ and 0.625 − 5 mg.mL⁻¹, respectively. Especially the ethyl acetate (EtOAc) extract displayed the highest activity (MIC = 0.3125 mg.mL⁻¹, MBC = 0.625 mg.mL⁻¹). Five known compounds (<b>1</b> − <b>5</b>) were obtained from the EtOAc extract of <i>Nemania</i> sp. LJZ-Y-11, and identified as chrysogeside D (<b>1</b>), 2-pyruvoylaminobenzamide (<b>2</b>), 4-hydroxybenzaldehyde (<b>3</b>), stigmasta-7,22-diene-3β,5ɑ,6α-triol (<b>4</b>), and (2<i>S</i>,5<i>R</i>)-2-ethyl-5-methylhexanedioic acid (<b>5</b>) based on spectroscopic analysis. Among them, compounds <b>3</b> and <b>5</b> showed significant inhibitory effects against Xcc, with MICs at 0.25 and 0.125 mg.mL⁻¹, respectively, and compound <b>5</b> showed more anti-Xcc potential with the MBC of 0.25 mg.mL⁻¹. The effects of compound <b>5</b> on the growth and cell morphology were dose-dependent and could reduce the formation of lesions or no lesions in leaves. Overall, the results indicated that citrus endophytic fungi could produce active products against the citrus canker pathogen, both crude extracts and compounds of the endophytic fungus <i>Nemania</i> sp. LJZ-Y-11 showed good anti-Xcc potential and encouraged further investigation of active compounds produced by citrus endophytic fungi.</p>