Background: Endophytic fungi have been recognized as new sources of natural products with a variety of biological activities, providing lead compounds for drug discovery and development. Objective: The objective of this study is to isolate and identify the secondary metabolites from the plant endophytic fungus Fusarium sp. HJY2 and evaluate their antibacterial activities. Methods: The compounds were isolated and purified by the methods of silica gel column chromatography, Sephadex LH-20 gel chromatography, and semi-preparative high performance liquid chromatography (HPLC). The structures of the isolated compounds were elucidated by comparing the NMR and MS spectroscopic data with those of pieces of literature. The antibacterial activities were evaluated by the broth microdilution method. Results: Seven polyketides were isolated from the fermented extracts of the fungus Fusarium sp. HJY2 and identified as sydowinol (1), dihydrolateropyrone (2), 13-oxo-9Z,11E-octadecadienoic acid (3), (E)-ferulic acid (4), 4-hydroxyphenylacetic acid (5), methyl 2-(2-hydroxyphenyl)acetate (6) and 4-hydroxy-3-methoxyacetophenone (7). Compound 3 exhibited moderate antibacterial activities against Bacillus subtilis, Mycobacterium smegmatis, Ralstonia solanacearum, and Xanthomonas campestris pv. campestris with MIC values of 40, 40, 80 and 40 μg/mL, respectively. Conclusion: Seven compounds were isolated from the plant endophytic fungus Fusarium sp. HJY2. Compound 1 was isolated from the Fusarium genus for the first time. Compound 3 showed moderate antibacterial activities.